1tuf - Revision history

OCA at 06:15, 3 April 2024

2024-04-03T06:15:40Z

←Older revision		Revision as of 06:15, 3 April 2024
Line 20:		Line 20:
	</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=1tuf 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=1tuf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Cocrystal structures of Methanococcus jannaschii diaminopimelate decarboxylase (DAPDC) bound to a substrate analog, azelaic acid, and its L-lysine product have been determined at 2.6 A and 2.0 A, respectively. This PLP-dependent enzyme is responsible for the final step of L-lysine biosynthesis in bacteria and plays a role in beta-lactam antibiotic resistance in Staphylococcus aureus. Substrate specificity derives from recognition of the L-chiral center of diaminopimelate and a system of ionic "molecular rulers" that dictate substrate length. A coupled-enzyme assay system permitted measurement of kinetic parameters for recombinant DAPDCs and inhibition constants (K(i)) for azelaic acid (89 microM) and other substrate analogs. Implications for rational design of broad-spectrum antimicrobial agents targeted against DAPDCs of drug-resistant strains of bacterial pathogens, such as Staphylococcus aureus, are discussed.
-
-	Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor.,Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK Structure. 2002 Nov;10(11):1499-508. PMID:12429091<ref>PMID:12429091</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1tuf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:06, 15 November 2023

2023-11-15T08:06:23Z

←Older revision		Revision as of 08:06, 15 November 2023
Line 3:		Line 3:
	<StructureSection load='1tuf' size='340' side='right'caption='[[1tuf]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1tuf' size='340' side='right'caption='[[1tuf]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43067 Atcc 43067~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1TUF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TUF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</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]] 2.4Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYSA, MJ1097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [https://pdbe.org/1tuf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [https://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tuf ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [~~http~~://pdbe.org/1tuf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1tuf ProSAT], [~~http~~://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DCDA_METJA DCDA_METJA]] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.<ref>PMID:12429091</ref>	+	[https://www.uniprot.org/uniprot/DCDA_METJA DCDA_METJA] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.<ref>PMID:12429091</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43067]]
-	[[Category: Diaminopimelate decarboxylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bonanno, J B~~]]	+	[[Category: Methanocaldococcus jannaschii]]
-	[[Category: ~~Burley, S K~~]]	+	[[Category: Bonanno JB]]
-	[[Category: ~~He, G~~]]	+	[[Category: Burley SK]]
-	[[Category: Lencastre, H De]]	+	[[Category: De Lencastre H]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: He G]]
-	[[Category: Pinho~~, M G~~]]	+	[[Category: Pinho MG]]
-	[[Category: Rajashankar, K]]	+	[[Category: Rajashankar K]]
-	[[Category: Ray~~, S R~~]]	+	[[Category: Ray SR]]
-	[[Category: Tomasz, A]]	+	[[Category: Tomasz A]]
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Diamnopimilate decarboxylase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Lysine biosynthesis]]~~	+
-	~~[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: T135~~]]	+

OCA at 12:00, 24 December 2020

2020-12-24T12:00:20Z

←Older revision		Revision as of 12:00, 24 December 2020
Line 1:		Line 1:

	==Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi==		==Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi==
-	<StructureSection load='1tuf' size='340' side='right' caption='[[1tuf]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1tuf' size='340' side='right'caption='[[1tuf]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1TUF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1TUF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYSA, MJ1097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYSA, MJ1097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://pdbe.org/1tuf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tuf ProSAT], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://pdbe.org/1tuf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tuf ProSAT], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 37:		Line 37:
	[[Category: Atcc 43067]]		[[Category: Atcc 43067]]
	[[Category: Diaminopimelate decarboxylase]]		[[Category: Diaminopimelate decarboxylase]]
		+	[[Category: Large Structures]]
	[[Category: Bonanno, J B]]		[[Category: Bonanno, J B]]
	[[Category: Burley, S K]]		[[Category: Burley, S K]]

OCA at 08:24, 21 March 2018

2018-03-21T08:24:12Z

←Older revision		Revision as of 08:24, 21 March 2018
Line 1:		Line 1:
		+
	==Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi==		==Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi==
	<StructureSection load='1tuf' size='340' side='right' caption='[[1tuf]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1tuf' size='340' side='right' caption='[[1tuf]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TUF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TUF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</scene></td></tr>
-	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-~~LYSINE(~~3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-~~YLMETHANE)~~'>LLP</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYSA, MJ1097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYSA, MJ1097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://pdbe.org/1tuf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://pdbe.org/1tuf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tuf ProSAT], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</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/tu/1tuf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tu/1tuf_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=1tuf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:47, 11 September 2015

2015-09-11T22:47:42Z

←Older revision		Revision as of 22:47, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1tuf' size='340' side='right' caption='[[1tuf]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1tuf' size='340' side='right' caption='[[1tuf]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanocaldococcus_jannaschii Methanocaldococcus jannaschii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TUF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TUF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYSA, MJ1097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ~~Methanocaldococcus jannaschii~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYSA, MJ1097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://pdbe.org/1tuf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</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 1tuf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43067]]
	[[Category: Diaminopimelate decarboxylase]]		[[Category: Diaminopimelate decarboxylase]]
-	[[Category: Methanocaldococcus jannaschii]]
	[[Category: Bonanno, J B]]		[[Category: Bonanno, J B]]
	[[Category: Burley, S K]]		[[Category: Burley, S K]]

OCA at 20:28, 25 December 2014

2014-12-25T20:28:16Z

←Older revision		Revision as of 20:28, 25 December 2014
Line 9:		Line 9:
	<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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DCDA_METJA DCDA_METJA]] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.<ref>PMID:12429091</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 13:11, 6 November 2014

2014-11-06T13:11:13Z

←Older revision		Revision as of 13:11, 6 November 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TUF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TUF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYSA, MJ1097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYSA, MJ1097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	[[Category: Diaminopimelate decarboxylase]]		[[Category: Diaminopimelate decarboxylase]]
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
-	[[Category: Bonanno, J B.]]	+	[[Category: Bonanno, J B]]
-	[[Category: Burley, S K.]]	+	[[Category: Burley, S K]]
-	[[Category: He, G.]]	+	[[Category: He, G]]
-	[[Category: Lencastre, H De.]]	+	[[Category: Lencastre, H De]]
-	[[Category: ~~NYSGXRC, New York SGX Research Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Pinho, M G.]]	+	[[Category: Pinho, M G]]
-	[[Category: Rajashankar, K.]]	+	[[Category: Rajashankar, K]]
-	[[Category: Ray, S R.]]	+	[[Category: Ray, S R]]
-	[[Category: Tomasz, A.]]	+	[[Category: Tomasz, A]]
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]
	[[Category: Diamnopimilate decarboxylase]]		[[Category: Diamnopimilate decarboxylase]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Lysine biosynthesis]]		[[Category: Lysine biosynthesis]]
-	[[Category: New ~~york sgx research center~~ for ~~structural genomic]]~~	+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
-	~~[[Category: Nysgxrc~~]]	+	[[Category: PSI, Protein structure initiative]]
-	[[Category: Protein structure initiative]]	+
-	~~[[Category: Psi]]~~	+
-	~~[[Category: Structural genomic~~]]	+
	[[Category: T135]]		[[Category: T135]]

OCA at 19:49, 29 September 2014

2014-09-29T19:49:30Z

←Older revision		Revision as of 19:49, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1tuf.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi==
		+	<StructureSection load='1tuf' size='340' side='right' caption='[[1tuf]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TUF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYSA, MJ1097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</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/tu/1tuf_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 ==
		+	Cocrystal structures of Methanococcus jannaschii diaminopimelate decarboxylase (DAPDC) bound to a substrate analog, azelaic acid, and its L-lysine product have been determined at 2.6 A and 2.0 A, respectively. This PLP-dependent enzyme is responsible for the final step of L-lysine biosynthesis in bacteria and plays a role in beta-lactam antibiotic resistance in Staphylococcus aureus. Substrate specificity derives from recognition of the L-chiral center of diaminopimelate and a system of ionic "molecular rulers" that dictate substrate length. A coupled-enzyme assay system permitted measurement of kinetic parameters for recombinant DAPDCs and inhibition constants (K(i)) for azelaic acid (89 microM) and other substrate analogs. Implications for rational design of broad-spectrum antimicrobial agents targeted against DAPDCs of drug-resistant strains of bacterial pathogens, such as Staphylococcus aureus, are discussed.

-	~~{{STRUCTURE_1tuf\| PDB=1tuf \| SCENE= }}~~	+	Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor.,Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK Structure. 2002 Nov;10(11):1499-508. PMID:12429091<ref>PMID:12429091</ref>

-	~~===Crystal structure~~ of ~~Diaminopimelate Decarboxylase from m~~. ~~jannaschi===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12429091}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1tuf]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012429091<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Diaminopimelate decarboxylase]]		[[Category: Diaminopimelate decarboxylase]]
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]

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

2013-01-05T13:09:53Z

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

←Older revision

Revision as of 13:09, 5 January 2013

OCA at 13:09, 5 January 2013

2013-01-05T13:09:50Z

←Older revision		Revision as of 13:09, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1tuf.png\|left\|200px]]		[[Image:1tuf.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1tuf", creates the "Structure Box" on the page.
-	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.
-	-->
	{{STRUCTURE_1tuf\| PDB=1tuf \| SCENE= }}		{{STRUCTURE_1tuf\| PDB=1tuf \| SCENE= }}

	===Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi===		===Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12429091}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12429091 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12429091}}		{{ABSTRACT_PUBMED_12429091}}

	==About this Structure==		==About this Structure==
-	~~1TUF~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA].	+	[[1tuf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12429091~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012429091</ref><references group="xtra"/>
	[[Category: Diaminopimelate decarboxylase]]		[[Category: Diaminopimelate decarboxylase]]
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
Line 30:		Line 18:
	[[Category: He, G.]]		[[Category: He, G.]]
	[[Category: Lencastre, H De.]]		[[Category: Lencastre, H De.]]
-	[[Category: NYSGXRC, New York ~~Structural GenomiX~~ Research ~~Consortium~~.]]	+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics.]]
	[[Category: Pinho, M G.]]		[[Category: Pinho, M G.]]
	[[Category: Rajashankar, K.]]		[[Category: Rajashankar, K.]]
Line 37:		Line 25:
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]
	[[Category: Diamnopimilate decarboxylase]]		[[Category: Diamnopimilate decarboxylase]]
		+	[[Category: Lyase]]
	[[Category: Lysine biosynthesis]]		[[Category: Lysine biosynthesis]]
-	[[Category: New york ~~structural genomix~~ research ~~consortium~~]]	+	[[Category: New york sgx research center for structural genomic]]
	[[Category: Nysgxrc]]		[[Category: Nysgxrc]]
	[[Category: Protein structure initiative]]		[[Category: Protein structure initiative]]
Line 44:		Line 33:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: T135]]		[[Category: T135]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:14:44 2009''