1tmm - Revision history

OCA at 13:30, 13 March 2024

OCA — Wed, 13 Mar 2024 13:30:13 GMT

←Older revision		Revision as of 13:30, 13 March 2024
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1tmm ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1tmm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Deletion mutagenesis, biochemical, and X-ray crystallographic studies have shown that loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is required for the assembly of the active center, plays an important role in the stabilization of the ternary complex of HPPK with MgATP and 6-hydroxymethyl-7,8-dihydropterin (HP), and is essential for catalysis. Whether the critical functional importance of loop 3 is due to the interactions between residues R84 and W89 and the two substrates has been addressed by site-directed mutagenesis, biochemical, and X-ray crystallographic studies. Substitution of R84 with alanine causes little changes in the dissociation constants and kinetic constants of the HPPK-catalyzed reaction, indicating that R84 is not important for either substrate binding or catalysis. Substitution of W89 with alanine increases the K(d) for the binding of MgATP by a factor of 3, whereas the K(d) for HP increases by a factor of 6, which is due to the increase in the dissociation rate constant. The W89A mutation decreases the rate constant for the chemical step of the forward reaction by a factor of 15 and the rate constant for the chemical step of the reverse reaction by a factor of 25. The biochemical results of the W89A mutation indicate that W89 contributes somewhat to the binding of HP and more significantly to the chemical step. The crystal structures of W89A show that W89A has different conformations in loops 2 and 3, but the critical catalytic residues are positioned for catalysis. When these results are taken together, they suggest that the critical functional importance of loop 3 is not due to the interactions of the R84 guanidinium group or the W89 indole ring with the substrates.
-
-	Is the critical role of loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase in catalysis due to loop-3 residues arginine-84 and tryptophan-89? Site-directed mutagenesis, biochemical, and crystallographic studies.,Li Y, Blaszczyk J, Wu Y, Shi G, Ji X, Yan H Biochemistry. 2005 Jun 21;44(24):8590-9. PMID:15952765<ref>PMID:15952765</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1tmm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[HPPK 3D structures\|HPPK 3D structures]]		*[[HPPK 3D structures\|HPPK 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:32, 23 August 2023

OCA — Wed, 23 Aug 2023 06:32:14 GMT

←Older revision		Revision as of 06:32, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1tmm' size='340' side='right'caption='[[1tmm]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1tmm' size='340' side='right'caption='[[1tmm]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tmm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TMM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tmm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TMM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.25Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1hka\|1hka]], [[1eqm\|1eqm]], [[1q0n\|1q0n]], [[1eq0\|1eq0]], [[1ex8\|1ex8]], [[1cbk\|1cbk]], [[1dy3\|1dy3]], [[1f9y\|1f9y]], [[1f9h\|1f9h]], [[1g4c\|1g4c]], [[1hq2\|1hq2]], [[1im6\|1im6]], [[1kbr\|1kbr]], [[1ru2\|1ru2]], [[1ru1\|1ru1]], [[1rtz\|1rtz]], [[1rb0\|1rb0]], [[1tmj\|1tmj]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [https://pdbe.org/1tmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [https://www.ebi.ac.uk/pdbsum/1tmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tmm ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [https://pdbe.org/1tmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [https://www.ebi.ac.uk/pdbsum/1tmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tmm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/HPPK_ECOLI HPPK_ECOLI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blaszczyk, J]]	+	[[Category: Blaszczyk J]]
-	[[Category: Ji, X]]	+	[[Category: Ji X]]
-	[[Category: Li, Y]]	+	[[Category: Li Y]]
-	[[Category: Shi, G]]	+	[[Category: Shi G]]
-	[[Category: Wu, Y]]	+	[[Category: Wu Y]]
-	[[Category: Yan, H]]	+	[[Category: Yan H]]
-	~~[[Category: 6-hydroxymethyl-7]]~~	+
-	~~[[Category: 6-hydroxymethylpterin]]~~	+
-	~~[[Category: 8-dihydropterin]]~~	+
-	~~[[Category: Antimicrobial agent]]~~	+
-	~~[[Category: Catalytic mechanism]]~~	+
-	~~[[Category: Drug design]]~~	+
-	~~[[Category: Folate]]~~	+
-	~~[[Category: Hppk]]~~	+
-	~~[[Category: Product release]]~~	+
-	~~[[Category: Pterin]]~~	+
-	~~[[Category: Pyrophosphokinase]]~~	+
-	~~[[Category: Pyrophosphoryl transfer]]~~	+
-	~~[[Category: Substrate specificity]]~~	+
-	~~[[Category: Ternary complex]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 15:42, 27 October 2021

OCA — Wed, 27 Oct 2021 15:42:33 GMT

←Older revision		Revision as of 15:42, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1tmm' size='340' side='right'caption='[[1tmm]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1tmm' size='340' side='right'caption='[[1tmm]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tmm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1TMM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tmm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TMM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1hka\|1hka]], [[1eqm\|1eqm]], [[1q0n\|1q0n]], [[1eq0\|1eq0]], [[1ex8\|1ex8]], [[1cbk\|1cbk]], [[1dy3\|1dy3]], [[1f9y\|1f9y]], [[1f9h\|1f9h]], [[1g4c\|1g4c]], [[1hq2\|1hq2]], [[1im6\|1im6]], [[1kbr\|1kbr]], [[1ru2\|1ru2]], [[1ru1\|1ru1]], [[1rtz\|1rtz]], [[1rb0\|1rb0]], [[1tmj\|1tmj]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1hka\|1hka]], [[1eqm\|1eqm]], [[1q0n\|1q0n]], [[1eq0\|1eq0]], [[1ex8\|1ex8]], [[1cbk\|1cbk]], [[1dy3\|1dy3]], [[1f9y\|1f9y]], [[1f9h\|1f9h]], [[1g4c\|1g4c]], [[1hq2\|1hq2]], [[1im6\|1im6]], [[1kbr\|1kbr]], [[1ru2\|1ru2]], [[1ru1\|1ru1]], [[1rtz\|1rtz]], [[1rb0\|1rb0]], [[1tmj\|1tmj]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [~~http~~://pdbe.org/1tmm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1tmm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1tmm ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [https://pdbe.org/1tmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [https://www.ebi.ac.uk/pdbsum/1tmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tmm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 11:55, 24 December 2020

OCA — Thu, 24 Dec 2020 11:55:57 GMT

←Older revision		Revision as of 11:55, 24 December 2020
Line 1:		Line 1:

	==Crystal structure of ternary complex of E.coli HPPK(W89A) with MGAMPCPP and 6-Hydroxymethylpterin==		==Crystal structure of ternary complex of E.coli HPPK(W89A) with MGAMPCPP and 6-Hydroxymethylpterin==
-	<StructureSection load='1tmm' size='340' side='right' caption='[[1tmm]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='1tmm' size='340' side='right'caption='[[1tmm]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tmm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1TMM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tmm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1TMM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hka\|1hka]], [[1eqm\|1eqm]], [[1q0n\|1q0n]], [[1eq0\|1eq0]], [[1ex8\|1ex8]], [[1cbk\|1cbk]], [[1dy3\|1dy3]], [[1f9y\|1f9y]], [[1f9h\|1f9h]], [[1g4c\|1g4c]], [[1hq2\|1hq2]], [[1im6\|1im6]], [[1kbr\|1kbr]], [[1ru2\|1ru2]], [[1ru1\|1ru1]], [[1rtz\|1rtz]], [[1rb0\|1rb0]], [[1tmj\|1tmj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1hka\|1hka]], [[1eqm\|1eqm]], [[1q0n\|1q0n]], [[1eq0\|1eq0]], [[1ex8\|1ex8]], [[1cbk\|1cbk]], [[1dy3\|1dy3]], [[1f9y\|1f9y]], [[1f9h\|1f9h]], [[1g4c\|1g4c]], [[1hq2\|1hq2]], [[1im6\|1im6]], [[1kbr\|1kbr]], [[1ru2\|1ru2]], [[1ru1\|1ru1]], [[1rtz\|1rtz]], [[1rb0\|1rb0]], [[1tmj\|1tmj]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [http://pdbe.org/1tmm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [http://www.ebi.ac.uk/pdbsum/1tmm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tmm ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [http://pdbe.org/1tmm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [http://www.ebi.ac.uk/pdbsum/1tmm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tmm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[~~6-hydroxymethyl-7%2C8-dihydropterin pyrophosphokinase~~\|~~6-hydroxymethyl-7%2C8-dihydropterin pyrophosphokinase~~]]	+	*[[HPPK 3D structures\|HPPK 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]		[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
		+	[[Category: Large Structures]]
	[[Category: Blaszczyk, J]]		[[Category: Blaszczyk, J]]
	[[Category: Ji, X]]		[[Category: Ji, X]]

OCA at 08:27, 21 March 2018

OCA — Wed, 21 Mar 2018 08:27:11 GMT

←Older revision		Revision as of 08:27, 21 March 2018
Line 1:		Line 1:
		+
	==Crystal structure of ternary complex of E.coli HPPK(W89A) with MGAMPCPP and 6-Hydroxymethylpterin==		==Crystal structure of ternary complex of E.coli HPPK(W89A) with MGAMPCPP and 6-Hydroxymethylpterin==
	<StructureSection load='1tmm' size='340' side='right' caption='[[1tmm]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1tmm' size='340' side='right' caption='[[1tmm]], [[Resolution\|resolution]] 1.25Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [http://pdbe.org/1tmm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [http://www.ebi.ac.uk/pdbsum/1tmm PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [http://pdbe.org/1tmm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [http://www.ebi.ac.uk/pdbsum/1tmm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tmm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tm/1tmm_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tm/1tmm_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1tmm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:26, 12 September 2015

OCA — Sat, 12 Sep 2015 00:26:05 GMT

←Older revision		Revision as of 00:26, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='1tmm' size='340' side='right' caption='[[1tmm]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1tmm' size='340' side='right' caption='[[1tmm]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tmm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TMM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tmm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TMM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hka\|1hka]], [[1eqm\|1eqm]], [[1q0n\|1q0n]], [[1eq0\|1eq0]], [[1ex8\|1ex8]], [[1cbk\|1cbk]], [[1dy3\|1dy3]], [[1f9y\|1f9y]], [[1f9h\|1f9h]], [[1g4c\|1g4c]], [[1hq2\|1hq2]], [[1im6\|1im6]], [[1kbr\|1kbr]], [[1ru2\|1ru2]], [[1ru1\|1ru1]], [[1rtz\|1rtz]], [[1rb0\|1rb0]], [[1tmj\|1tmj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hka\|1hka]], [[1eqm\|1eqm]], [[1q0n\|1q0n]], [[1eq0\|1eq0]], [[1ex8\|1ex8]], [[1cbk\|1cbk]], [[1dy3\|1dy3]], [[1f9y\|1f9y]], [[1f9h\|1f9h]], [[1g4c\|1g4c]], [[1hq2\|1hq2]], [[1im6\|1im6]], [[1kbr\|1kbr]], [[1ru2\|1ru2]], [[1ru1\|1ru1]], [[1rtz\|1rtz]], [[1rb0\|1rb0]], [[1tmj\|1tmj]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [http://www.ebi.ac.uk/pdbsum/1tmm PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [http://pdbe.org/1tmm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [http://www.ebi.ac.uk/pdbsum/1tmm PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1tmm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]		[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
-	[[Category: Escherichia coli]]
	[[Category: Blaszczyk, J]]		[[Category: Blaszczyk, J]]
	[[Category: Ji, X]]		[[Category: Ji, X]]

OCA at 13:23, 6 January 2015

OCA — Tue, 06 Jan 2015 13:23:01 GMT

←Older revision		Revision as of 13:23, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tmm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TMM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tmm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TMM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hka\|1hka]], [[1eqm\|1eqm]], [[1q0n\|1q0n]], [[1eq0\|1eq0]], [[1ex8\|1ex8]], [[1cbk\|1cbk]], [[1dy3\|1dy3]], [[1f9y\|1f9y]], [[1f9h\|1f9h]], [[1g4c\|1g4c]], [[1hq2\|1hq2]], [[1im6\|1im6]], [[1kbr\|1kbr]], [[1ru2\|1ru2]], [[1ru1\|1ru1]], [[1rtz\|1rtz]], [[1rb0\|1rb0]], [[1tmj\|1tmj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hka\|1hka]], [[1eqm\|1eqm]], [[1q0n\|1q0n]], [[1eq0\|1eq0]], [[1ex8\|1ex8]], [[1cbk\|1cbk]], [[1dy3\|1dy3]], [[1f9y\|1f9y]], [[1f9h\|1f9h]], [[1g4c\|1g4c]], [[1hq2\|1hq2]], [[1im6\|1im6]], [[1kbr\|1kbr]], [[1ru2\|1ru2]], [[1ru1\|1ru1]], [[1rtz\|1rtz]], [[1rb0\|1rb0]], [[1tmj\|1tmj]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [http://www.ebi.ac.uk/pdbsum/1tmm PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [http://www.ebi.ac.uk/pdbsum/1tmm PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]		[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Blaszczyk, J.]]	+	[[Category: Blaszczyk, J]]
-	[[Category: Ji, X.]]	+	[[Category: Ji, X]]
-	[[Category: Li, Y.]]	+	[[Category: Li, Y]]
-	[[Category: Shi, G.]]	+	[[Category: Shi, G]]
-	[[Category: Wu, Y.]]	+	[[Category: Wu, Y]]
-	[[Category: Yan, H.]]	+	[[Category: Yan, H]]
	[[Category: 6-hydroxymethyl-7]]		[[Category: 6-hydroxymethyl-7]]
	[[Category: 6-hydroxymethylpterin]]		[[Category: 6-hydroxymethylpterin]]

OCA at 20:48, 29 September 2014

OCA — Mon, 29 Sep 2014 20:48:57 GMT

←Older revision		Revision as of 20:48, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1tmm.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of ternary complex of E.coli HPPK(W89A) with MGAMPCPP and 6-Hydroxymethylpterin==
		+	<StructureSection load='1tmm' size='340' side='right' caption='[[1tmm]], [[Resolution\|resolution]] 1.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1tmm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TMM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HHR:6-HYDROXYMETHYLPTERIN'>HHR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hka\|1hka]], [[1eqm\|1eqm]], [[1q0n\|1q0n]], [[1eq0\|1eq0]], [[1ex8\|1ex8]], [[1cbk\|1cbk]], [[1dy3\|1dy3]], [[1f9y\|1f9y]], [[1f9h\|1f9h]], [[1g4c\|1g4c]], [[1hq2\|1hq2]], [[1im6\|1im6]], [[1kbr\|1kbr]], [[1ru2\|1ru2]], [[1ru1\|1ru1]], [[1rtz\|1rtz]], [[1rb0\|1rb0]], [[1tmj\|1tmj]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FOLK, B0142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tmm RCSB], [http://www.ebi.ac.uk/pdbsum/1tmm PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tm/1tmm_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Deletion mutagenesis, biochemical, and X-ray crystallographic studies have shown that loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is required for the assembly of the active center, plays an important role in the stabilization of the ternary complex of HPPK with MgATP and 6-hydroxymethyl-7,8-dihydropterin (HP), and is essential for catalysis. Whether the critical functional importance of loop 3 is due to the interactions between residues R84 and W89 and the two substrates has been addressed by site-directed mutagenesis, biochemical, and X-ray crystallographic studies. Substitution of R84 with alanine causes little changes in the dissociation constants and kinetic constants of the HPPK-catalyzed reaction, indicating that R84 is not important for either substrate binding or catalysis. Substitution of W89 with alanine increases the K(d) for the binding of MgATP by a factor of 3, whereas the K(d) for HP increases by a factor of 6, which is due to the increase in the dissociation rate constant. The W89A mutation decreases the rate constant for the chemical step of the forward reaction by a factor of 15 and the rate constant for the chemical step of the reverse reaction by a factor of 25. The biochemical results of the W89A mutation indicate that W89 contributes somewhat to the binding of HP and more significantly to the chemical step. The crystal structures of W89A show that W89A has different conformations in loops 2 and 3, but the critical catalytic residues are positioned for catalysis. When these results are taken together, they suggest that the critical functional importance of loop 3 is not due to the interactions of the R84 guanidinium group or the W89 indole ring with the substrates.

-	~~{{STRUCTURE_1tmm\| PDB=1tmm \| SCENE= }}~~	+	Is the critical role of loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase in catalysis due to loop-3 residues arginine-84 and tryptophan-89? Site-directed mutagenesis, biochemical, and crystallographic studies.,Li Y, Blaszczyk J, Wu Y, Shi G, Ji X, Yan H Biochemistry. 2005 Jun 21;44(24):8590-9. PMID:15952765<ref>PMID:15952765</ref>

-	~~===Crystal structure~~ of ~~ternary complex~~ of E.~~coli HPPK(W89A) with MGAMPCPP and 6-Hydroxymethylpterin===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_15952765}}~~	+	==See Also==
-		+	*[[6-hydroxymethyl-7%2C8-dihydropterin pyrophosphokinase\|6-hydroxymethyl-7%2C8-dihydropterin pyrophosphokinase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1tmm~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMM OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:015952765<~~/~~ref~~><~~ref group="xtra">PMID:010378268</ref><references group="xtra"~~/>	+
	[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]		[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 09:31, 16 January 2013

OCA — Wed, 16 Jan 2013 09:31:56 GMT

←Older revision		Revision as of 09:31, 16 January 2013
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	[[Image:1tmm.png\|left\|200px]]		[[Image:1tmm.png\|left\|200px]]

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	{{STRUCTURE_1tmm\| PDB=1tmm \| SCENE= }}		{{STRUCTURE_1tmm\| PDB=1tmm \| SCENE= }}

	===Crystal structure of ternary complex of E.coli HPPK(W89A) with MGAMPCPP and 6-Hydroxymethylpterin===		===Crystal structure of ternary complex of E.coli HPPK(W89A) with MGAMPCPP and 6-Hydroxymethylpterin===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15952765}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15952765 is the PubMed ID number.
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	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15952765~~</ref><ref group="xtra">PMID:~~10378268</ref><ref group="xtra">PMID:11080626</ref><ref group="xtra">PMID:11311059~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015952765</ref><ref group="xtra">PMID:010378268</ref><references group="xtra"/>
	[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]		[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
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	[[Category: Ternary complex]]		[[Category: Ternary complex]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	[[Category: X-ray crystallography]]

OCA: Protected "1tmm" [edit=sysop:move=sysop]

OCA — Mon, 14 Mar 2011 19:44:31 GMT

Protected "1tmm" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:44, 14 March 2011