1e4e - Revision history

OCA at 07:14, 9 October 2024

2024-10-09T07:14:13Z

← Older revision		Revision as of 07:14, 9 October 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e4/1e4e_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e4/1e4e_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 11:52, 13 December 2023

2023-12-13T11:52:25Z

← Older revision		Revision as of 11:52, 13 December 2023
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	<StructureSection load='1e4e' size='340' side='right'caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1e4e' size='340' side='right'caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_19434 Atcc 19434~~]. The December 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vancomycin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_12 10.2210/rcsb_pdb/mom_2015_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. The December 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vancomycin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_12 10.2210/rcsb_pdb/mom_2015_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene>, <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]] 2.5Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1iow\|1iow]], [[1iov\|1iov]]</div></td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VANA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1352 ATCC 19434])</td></tr>~~
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-alanine--(R)-lactate_ligase D-alanine--(R)-lactate ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.2.1 6.1.2.1] </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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [https://pdbe.org/1e4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [https://www.ebi.ac.uk/pdbsum/1e4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e4e 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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [https://pdbe.org/1e4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [https://www.ebi.ac.uk/pdbsum/1e4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/VANA_ENTFC VANA_ENTFC]] Required for high-level resistance to glycopeptide antibiotics. D-Ala--D-Ala ligase of altered specificity which catalyzes ester bond formation between D-Ala and various D-hydroxy acids; produces a peptidoglycan which does not terminate in D-alanine but in D-lactate, thus preventing vancomycin or teicoplanin binding.<ref>PMID:1931965</ref>		[https://www.uniprot.org/uniprot/VANA_ENTFC VANA_ENTFC] Required for high-level resistance to glycopeptide antibiotics. D-Ala--D-Ala ligase of altered specificity which catalyzes ester bond formation between D-Ala and various D-hydroxy acids; produces a peptidoglycan which does not terminate in D-alanine but in D-lactate, thus preventing vancomycin or teicoplanin binding.<ref>PMID:1931965</ref>
	== 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: ~~Atcc 19434~~]]		[[Category: Enterococcus faecium]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Vancomycin]]		[[Category: Vancomycin]]
	[[Category: Roper~~, D I]]~~		[[Category: Roper DI]]
	~~[[Category: Antibiotic resistance]]~~
	~~[[Category: Cell wall]]~~
	~~[[Category: Ligase]]~~
	~~[[Category: Membrane]]~~
	~~[[Category: Peptidoglycan synthesis~~]]

OCA at 10:46, 14 July 2021

2021-07-14T10:46:59Z

OCA at 05:30, 10 October 2019

2019-10-10T05:30:49Z

← Older revision		Revision as of 05:30, 10 October 2019
Line 1:		Line 1:

	==D-alanyl-D-lacate ligase==		==D-alanyl-D-lacate ligase==
	<StructureSection load='1e4e' size='340' side='right' caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1e4e' size='340' side='right'caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. The December 2015 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vancomycin'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2015_12 10.2210/rcsb_pdb/mom_2015_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. The December 2015 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vancomycin'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2015_12 10.2210/rcsb_pdb/mom_2015_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E4E FirstGlance]. <br>
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e4/1e4e_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e4/1e4e_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>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 19434]]		[[Category: Atcc 19434]]
			[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Vancomycin]]		[[Category: Vancomycin]]

OCA at 05:38, 6 October 2017

2017-10-06T05:38:01Z

← Older revision		Revision as of 05:38, 6 October 2017
Line 1:		Line 1:
	==D-~~ALANYL~~-D-~~LACATE LIGASE~~==
			==D-alanyl-D-lacate ligase==
	<StructureSection load='1e4e' size='340' side='right' caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1e4e' size='340' side='right' caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VANA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1352 ATCC 19434])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VANA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1352 ATCC 19434])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--(R)-lactate_ligase D-alanine--(R)-lactate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.2.1 6.1.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--(R)-lactate_ligase D-alanine--(R)-lactate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.2.1 6.1.2.1] </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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [http://pdbe.org/1e4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [http://www.ebi.ac.uk/pdbsum/1e4e 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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [http://pdbe.org/1e4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [http://www.ebi.ac.uk/pdbsum/1e4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 21:02, 9 February 2016

2016-02-09T21:02:34Z

← Older revision		Revision as of 21:02, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='1e4e' size='340' side='right' caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1e4e' size='340' side='right' caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. The December 2015 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vancomycin'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2015_12 10.2210/rcsb_pdb/mom_2015_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene>, <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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene>, <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">[[1iow\|1iow]], [[1iov\|1iov]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iow\|1iow]], [[1iov\|1iov]]</td></tr>
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=1e4e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 19434]]		[[Category: Atcc 19434]]
			[[Category: RCSB PDB Molecule of the Month]]
			[[Category: Vancomycin]]
	[[Category: Roper, D I]]		[[Category: Roper, D I]]
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]

OCA at 02:00, 11 September 2015

2015-09-11T02:00:18Z

← Older revision		Revision as of 02:00, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1e4e' size='340' side='right' caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1e4e' size='340' side='right' caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterococcus_faecium Enterococcus faecium~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene>, <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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene>, <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">[[1iow\|1iow]], [[1iov\|1iov]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iow\|1iow]], [[1iov\|1iov]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VANA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1352 ~~Enterococcus faecium~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VANA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1352 ATCC 19434])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--(R)-lactate_ligase D-alanine--(R)-lactate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.2.1 6.1.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--(R)-lactate_ligase D-alanine--(R)-lactate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.2.1 6.1.2.1] </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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [http://www.ebi.ac.uk/pdbsum/1e4e 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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [http://pdbe.org/1e4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [http://www.ebi.ac.uk/pdbsum/1e4e 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 1e4e" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Enterococcus faecium~~]]		[[Category: Atcc 19434]]
	[[Category: Roper, D I]]		[[Category: Roper, D I]]
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]

OCA at 09:31, 25 December 2014

2014-12-25T09:31:18Z

← Older revision		Revision as of 09:31, 25 December 2014
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	<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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [http://www.ebi.ac.uk/pdbsum/1e4e 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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [http://www.ebi.ac.uk/pdbsum/1e4e PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/VANA_ENTFC VANA_ENTFC]] Required for high-level resistance to glycopeptide antibiotics. D-Ala--D-Ala ligase of altered specificity which catalyzes ester bond formation between D-Ala and various D-hydroxy acids; produces a peptidoglycan which does not terminate in D-alanine but in D-lactate, thus preventing vancomycin or teicoplanin binding.<ref>PMID:1931965</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 22:18, 22 December 2014

2014-12-22T22:18:35Z

← Older revision		Revision as of 22:18, 22 December 2014
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E4E FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene>, <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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iow\|1iow]], [[1iov\|1iov]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iow\|1iow]], [[1iov\|1iov]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VANA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1352 Enterococcus faecium])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VANA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1352 Enterococcus faecium])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--(R)-lactate_ligase D-alanine--(R)-lactate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.2.1 6.1.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--(R)-lactate_ligase D-alanine--(R)-lactate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.2.1 6.1.2.1] </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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [http://www.ebi.ac.uk/pdbsum/1e4e 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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [http://www.ebi.ac.uk/pdbsum/1e4e PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Enterococcus faecium]]		[[Category: Enterococcus faecium]]
	[[Category: Roper, D I.]]		[[Category: Roper, D I]]
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]
	[[Category: Cell wall]]		[[Category: Cell wall]]

OCA at 10:29, 3 October 2014

2014-10-03T10:29:29Z

← Older revision		Revision as of 10:29, 3 October 2014
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	~~{{STRUCTURE_1e4e~~\| ~~PDB~~=1e4e \| ~~SCENE~~= }}		==D-ALANYL-D-LACATE LIGASE==
	===D-~~ALANYL~~-D-~~LACATE LIGASE~~===		<StructureSection load='1e4e' size='340' side='right' caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>
	~~{{ABSTRACT_PUBMED_10908650}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E4E FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iow\|1iow]], [[1iov\|1iov]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VANA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1352 Enterococcus faecium])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--(R)-lactate_ligase D-alanine--(R)-lactate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.2.1 6.1.2.1] </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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [http://www.ebi.ac.uk/pdbsum/1e4e 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/e4/1e4e_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 ==
			d-alanine-d-lactate ligase from Enterococcus faecium BM4147 is directly responsible for the biosynthesis of alternate cell-wall precursors in bacteria, which are resistant to the glycopeptide antibiotic vancomycin. The crystal structure has been determined with data extending to 2.5-A resolution. This structure shows that the active site has unexpected interactions and is distinct from previous models for d-alanyl-d-lactate ligase mechanistic studies. It appears that the preference of the enzyme for lactate as a ligand over d-alanine could be mediated by electrostatic effects and/or a hydrogen-bonding network, which principally involve His-244. The structure of d-alanyl-d-lactate ligase provides a revised interpretation of the molecular events that lead to vancomycin resistance.

	~~==Function==~~		The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA).,Roper DI, Huyton T, Vagin A, Dodson G Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):8921-5. PMID:10908650<ref>PMID:10908650</ref>
	~~[[http~~:~~//www.uniprot.org/uniprot/VANA_ENTFC VANA_ENTFC]] Required for high-level resistance to glycopeptide antibiotics.~~ D-~~Ala-~~-D-~~Ala~~ ligase ~~of altered specificity which catalyzes ester bond formation between D-Ala and various D-hydroxy acids~~; ~~produces a peptidoglycan which does not terminate in D~~-~~alanine but in D-lactate, thus preventing vancomycin or teicoplanin binding~~.<ref>PMID:~~1931965~~</ref>

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[1e4e]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterococcus_faecium Enterococcus faecium]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA].~~		</div>
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:010908650</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Enterococcus faecium]]		[[Category: Enterococcus faecium]]
	[[Category: Roper, D I.]]		[[Category: Roper, D I.]]

← Older revision		Revision as of 10:46, 14 July 2021
Line 3:		Line 3:
	<StructureSection load='1e4e' size='340' side='right'caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1e4e' size='340' side='right'caption='[[1e4e]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. The December 2015 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vancomycin'' by David Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2015_12 10.2210/rcsb_pdb/mom_2015_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. The December 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vancomycin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_12 10.2210/rcsb_pdb/mom_2015_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene>, <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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene>, <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">[[1iow\|1iow]], [[1iov\|1iov]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1iow\|1iow]], [[1iov\|1iov]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VANA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1352 ATCC 19434])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VANA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1352 ATCC 19434])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/D-alanine--(R)-lactate_ligase D-alanine--(R)-lactate ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.2.1 6.1.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-alanine--(R)-lactate_ligase D-alanine--(R)-lactate ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.2.1 6.1.2.1] </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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [~~http~~://pdbe.org/1e4e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1e4e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1e4e 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=1e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e4e OCA], [https://pdbe.org/1e4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e4e RCSB], [https://www.ebi.ac.uk/pdbsum/1e4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/VANA_ENTFC VANA_ENTFC]] Required for high-level resistance to glycopeptide antibiotics. D-Ala--D-Ala ligase of altered specificity which catalyzes ester bond formation between D-Ala and various D-hydroxy acids; produces a peptidoglycan which does not terminate in D-alanine but in D-lactate, thus preventing vancomycin or teicoplanin binding.<ref>PMID:1931965</ref>		[[https://www.uniprot.org/uniprot/VANA_ENTFC VANA_ENTFC]] Required for high-level resistance to glycopeptide antibiotics. D-Ala--D-Ala ligase of altered specificity which catalyzes ester bond formation between D-Ala and various D-hydroxy acids; produces a peptidoglycan which does not terminate in D-alanine but in D-lactate, thus preventing vancomycin or teicoplanin binding.<ref>PMID:1931965</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]