1kdp - Revision history

OCA at 18:12, 29 May 2024

2024-05-29T18:12:55Z

←Older revision		Revision as of 18:12, 29 May 2024
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	<table><tr><td colspan='2'>[[1kdp]] 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=1KDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KDP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kdp]] 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=1KDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KDP FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</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]] 2.3Å</td></tr>
-	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [https://pdbe.org/1kdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [https://www.ebi.ac.uk/pdbsum/1kdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdp 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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [https://pdbe.org/1kdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [https://www.ebi.ac.uk/pdbsum/1kdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdp ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:56, 16 August 2023

2023-08-16T08:56:07Z

←Older revision		Revision as of 08:56, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1kdp' size='340' side='right'caption='[[1kdp]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1kdp' size='340' side='right'caption='[[1kdp]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kdp]] 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=1KDP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1KDP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kdp]] 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=1KDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KDP FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1kdo\|1kdo]]~~, [[~~1kdr~~\|~~1kdr]], [[1kdt\|1kdt~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>cmk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [https://pdbe.org/1kdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [https://www.ebi.ac.uk/pdbsum/1kdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdp ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14]~~ </~~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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [~~http~~://pdbe.org/1kdp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kdp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdp ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KCY_ECOLI KCY_ECOLI]] ATP, dATP, and GTP are equally effective as phosphate donors. CMP and dCMP are the best phosphate acceptors.<ref>PMID:8190075</ref> <ref>PMID:7836281</ref>	+	[https://www.uniprot.org/uniprot/KCY_ECOLI KCY_ECOLI] ATP, dATP, and GTP are equally effective as phosphate donors. CMP and dCMP are the best phosphate acceptors.<ref>PMID:8190075</ref> <ref>PMID:7836281</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: UMP/CMP kinase]]~~	+	[[Category: Assairi L]]
-	[[Category: Assairi, L]]	+	[[Category: Barzu O]]
-	[[Category: Barzu, O]]	+	[[Category: Bertrand T]]
-	[[Category: Bertrand, T]]	+	[[Category: Briozzo P]]
-	[[Category: Briozzo, P]]	+	[[Category: Bucurenci N]]
-	[[Category: Bucurenci, N]]	+	[[Category: Gilles AM]]
-	[[Category: Gilles~~, A M~~]]	+	[[Category: Golinelli-Pimpaneau B]]
-	[[Category: Golinelli-Pimpaneau, B]]	+	[[Category: Munier-Lehmann H]]
-	[[Category: Munier-Lehmann, H]]	+	[[Category: Ofiteru A]]
-	[[Category: Ofiteru, A]]	+
-	~~[[Category: Nucleotide monophosphate kinase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:43, 25 November 2020

2020-11-25T07:43:38Z

←Older revision		Revision as of 07:43, 25 November 2020
Line 1:		Line 1:

	==CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEOXY-CYTIDINE MONOPHOSPHATE==		==CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEOXY-CYTIDINE MONOPHOSPHATE==
-	<StructureSection load='1kdp' size='340' side='right' caption='[[1kdp]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1kdp' size='340' side='right'caption='[[1kdp]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kdp]] 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=1KDP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KDP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kdp]] 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=1KDP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1KDP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kdo\|1kdo]], [[1kdr\|1kdr]], [[1kdt\|1kdt]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kdo\|1kdo]], [[1kdr\|1kdr]], [[1kdt\|1kdt]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmk ([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">cmk ([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/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [http://pdbe.org/1kdp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [http://www.ebi.ac.uk/pdbsum/1kdp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdp 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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [http://pdbe.org/1kdp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [http://www.ebi.ac.uk/pdbsum/1kdp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: UMP/CMP kinase]]		[[Category: UMP/CMP kinase]]
	[[Category: Assairi, L]]		[[Category: Assairi, L]]

OCA at 21:20, 24 January 2018

2018-01-24T21:20:46Z

←Older revision		Revision as of 21:20, 24 January 2018
Line 1:		Line 1:
		+
	==CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEOXY-CYTIDINE MONOPHOSPHATE==		==CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEOXY-CYTIDINE MONOPHOSPHATE==
	<StructureSection load='1kdp' size='340' side='right' caption='[[1kdp]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1kdp' size='340' side='right' caption='[[1kdp]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmk ([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">cmk ([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/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [http://pdbe.org/1kdp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [http://www.ebi.ac.uk/pdbsum/1kdp 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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [http://pdbe.org/1kdp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [http://www.ebi.ac.uk/pdbsum/1kdp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/1kdp_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/1kdp_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>

OCA at 02:48, 10 February 2016

2016-02-10T02:48:00Z

←Older revision		Revision as of 02:48, 10 February 2016
Line 19:		Line 19:
	<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=1kdp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:37, 11 September 2015

2015-09-11T04:37:47Z

←Older revision		Revision as of 04:37, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1kdp' size='340' side='right' caption='[[1kdp]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1kdp' size='340' side='right' caption='[[1kdp]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kdp]] 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=1KDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kdp]] 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=1KDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kdo\|1kdo]], [[1kdr\|1kdr]], [[1kdt\|1kdt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kdo\|1kdo]], [[1kdr\|1kdr]], [[1kdt\|1kdt]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmk ([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">cmk ([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/~~Cytidylate_kinase Cytidylate~~ kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [http://www.ebi.ac.uk/pdbsum/1kdp 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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [http://pdbe.org/1kdp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [http://www.ebi.ac.uk/pdbsum/1kdp PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1kdp" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cytidylate kinase~~]]	+	[[Category: Bacillus coli migula 1895]]
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: UMP/CMP kinase]]
	[[Category: Assairi, L]]		[[Category: Assairi, L]]
	[[Category: Barzu, O]]		[[Category: Barzu, O]]

OCA at 11:15, 25 December 2014

2014-12-25T11:15:45Z

←Older revision		Revision as of 11:15, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kdp]] 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=1KDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kdp]] 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=1KDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDP FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kdo\|1kdo]], [[1kdr\|1kdr]], [[1kdt\|1kdt]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kdo\|1kdo]], [[1kdr\|1kdr]], [[1kdt\|1kdt]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmk ([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">cmk ([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/Cytidylate_kinase Cytidylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytidylate_kinase Cytidylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [http://www.ebi.ac.uk/pdbsum/1kdp 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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [http://www.ebi.ac.uk/pdbsum/1kdp PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KCY_ECOLI KCY_ECOLI]] ATP, dATP, and GTP are equally effective as phosphate donors. CMP and dCMP are the best phosphate acceptors.<ref>PMID:8190075</ref> <ref>PMID:7836281</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Cytidylate kinase]]		[[Category: Cytidylate kinase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Assairi, L.]]	+	[[Category: Assairi, L]]
-	[[Category: Barzu, O.]]	+	[[Category: Barzu, O]]
-	[[Category: Bertrand, T.]]	+	[[Category: Bertrand, T]]
-	[[Category: Briozzo, P.]]	+	[[Category: Briozzo, P]]
-	[[Category: Bucurenci, N.]]	+	[[Category: Bucurenci, N]]
-	[[Category: Gilles, A M.]]	+	[[Category: Gilles, A M]]
-	[[Category: Golinelli-Pimpaneau, B.]]	+	[[Category: Golinelli-Pimpaneau, B]]
-	[[Category: Munier-Lehmann, H.]]	+	[[Category: Munier-Lehmann, H]]
-	[[Category: Ofiteru, A.]]	+	[[Category: Ofiteru, A]]
	[[Category: Nucleotide monophosphate kinase]]		[[Category: Nucleotide monophosphate kinase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 08:29, 28 September 2014

2014-09-28T08:29:27Z

←Older revision		Revision as of 08:29, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1kdp.~~png~~\|~~left~~\|200px]]	+	==CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEOXY-CYTIDINE MONOPHOSPHATE==
		+	<StructureSection load='1kdp' size='340' side='right' caption='[[1kdp]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kdp]] 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=1KDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDP FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kdo\|1kdo]], [[1kdr\|1kdr]], [[1kdt\|1kdt]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmk ([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/Cytidylate_kinase Cytidylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </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=1kdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kdp RCSB], [http://www.ebi.ac.uk/pdbsum/1kdp 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/kd/1kdp_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 ==
		+	Bacterial cytidine monophosphate (CMP) kinases are characterised by an insert enlarging their CMP binding domain, and by their particular substrate specificity. Thus, both CMP and 2'-deoxy-CMP (dCMP) are good phosphate acceptors for the CMP kinase from Escherichia coli (E. coli CMPK), whereas eukaryotic UMP/CMP kinases phosphorylate the deoxynucleotides with very low efficiency. Four crystal structures of E. coli CMPK complexed with nucleoside monophosphates differing in their sugar moiety were solved. Both structures with CMP or dCMP show interactions with the pentose that were not described so far. These interactions are lost with the poorer substrates AraCMP and 2',3'-dideoxy-CMP. Comparison of all four structures shows that the pentose hydroxyls are involved in ligand-induced movements of enzyme domains. It also gives a structural basis of the mechanism by which either ribose or deoxyribose can be accommodated. In parallel, for the four nucleotides the kinetic results of the wild-type enzyme and of three structure-based variants are presented. The phosphorylation rate is significantly decreased when either of the two pentose interacting residues is mutated. One of these is an arginine that is highly conserved in all known nucleoside monophosphate kinases. In contrast, the other residue, Asp185, is typical of bacterial CMP kinases. It interacts with Ser101, the only residue conserved in all CMP binding domain inserts. Mutating Ser101 reduces CMP phosphorylation only moderately, but dramatically reduces dCMP phosphorylation. This is the first experimental evidence of a catalytic role involving the characteristic insert of bacterial CMP kinases. Furthermore, this role concerns only dCMP phosphorylation, a feature of this family of enzymes.

-	~~{{STRUCTURE_1kdp\| PDB=1kdp \| SCENE= }}~~	+	Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme.,Bertrand T, Briozzo P, Assairi L, Ofiteru A, Bucurenci N, Munier-Lehmann H, Golinelli-Pimpaneau B, Barzu O, Gilles AM J Mol Biol. 2002 Feb 1;315(5):1099-110. PMID:11827479<ref>PMID:11827479</ref>

-	~~===CYTIDINE MONOPHOSPHATE KINASE FROM E~~. ~~COLI IN COMPLEX WITH 2'-DEOXY-CYTIDINE MONOPHOSPHATE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_11827479}}~~	+	==See Also==
-		+	*[[Cytidine monophosphate kinase\|Cytidine monophosphate kinase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1kdp~~]] 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=1KDP OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:011827479<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Cytidylate kinase]]		[[Category: Cytidylate kinase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

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

2012-12-05T19:47:03Z

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

←Older revision

Revision as of 19:47, 5 December 2012

OCA at 19:46, 5 December 2012

2012-12-05T19:46:59Z

←Older revision		Revision as of 19:46, 5 December 2012
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-	{{Seed}}
	[[Image:1kdp.png\|left\|200px]]		[[Image:1kdp.png\|left\|200px]]

-	<!--
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-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
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	{{STRUCTURE_1kdp\| PDB=1kdp \| SCENE= }}		{{STRUCTURE_1kdp\| PDB=1kdp \| SCENE= }}

	===CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEOXY-CYTIDINE MONOPHOSPHATE===		===CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEOXY-CYTIDINE MONOPHOSPHATE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11827479}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11827479 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_11827479}}		{{ABSTRACT_PUBMED_11827479}}

	==About this Structure==		==About this Structure==
-	~~1KDP~~ is a 2 ~~chains~~ structure ~~of sequences~~ 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=1KDP OCA].	+	[[1kdp]] 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=1KDP OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11827479~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011827479</ref><references group="xtra"/>
	[[Category: Cytidylate kinase]]		[[Category: Cytidylate kinase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 37:		Line 25:
	[[Category: Nucleotide monophosphate kinase]]		[[Category: Nucleotide monophosphate kinase]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:48:20 2009''