1iki - Revision history

OCA at 08:35, 16 August 2023

2023-08-16T08:35:04Z

←Older revision		Revision as of 08:35, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1iki' size='340' side='right'caption='[[1iki]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1iki' size='340' side='right'caption='[[1iki]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IKI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._R61 Streptomyces sp. R61]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IKI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DAL:D~~-~~ALANINE'>DAL</scene>~~, ~~<scene name='pdbligand=REY:GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE'>REY</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.25Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1ikg\|1ikg]], [[1hvb\|1hvb]], [[3pte\|3pte]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REY:GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE'>REY</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Serine~~-~~type_D~~-~~Ala~~-D-~~Ala_carboxypeptidase Serine~~-~~type D-Ala~~-D-~~Ala carboxypeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4]~~ </~~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=1iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iki OCA], [https://pdbe.org/1iki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iki RCSB], [https://www.ebi.ac.uk/pdbsum/1iki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iki 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=1iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iki OCA], [https://pdbe.org/1iki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iki RCSB], [https://www.ebi.ac.uk/pdbsum/1iki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iki ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DAC_STRSR DAC_STRSR]] Catalyzes distinct carboxypeptidation and transpeptidation reactions during the last stages of wall peptidoglycan synthesis. Mistaking a beta-lactam antibiotic molecule for a normal substrate (i.e. a D-alanyl-D-alanine-terminated peptide), it becomes immobilized in the form of a long-lived, serine-ester-linked acyl enzyme and thus behave as penicillin-binding protein (PBP).	+	[https://www.uniprot.org/uniprot/DAC_STRSR DAC_STRSR] Catalyzes distinct carboxypeptidation and transpeptidation reactions during the last stages of wall peptidoglycan synthesis. Mistaking a beta-lactam antibiotic molecule for a normal substrate (i.e. a D-alanyl-D-alanine-terminated peptide), it becomes immobilized in the form of a long-lived, serine-ester-linked acyl enzyme and thus behave as penicillin-binding protein (PBP).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]~~	+	[[Category: Streptomyces sp. R61]]
-	[[Category: Streptomyces sp]]	+	[[Category: Anderson JW]]
-	[[Category: Anderson~~, J W~~]]	+	[[Category: Kelly JA]]
-	[[Category: Kelly~~, J A~~]]	+	[[Category: Knox JR]]
-	[[Category: Knox~~, J R~~]]	+	[[Category: Mcdonough MA]]
-	[[Category: Mcdonough~~, M A~~]]	+	[[Category: Pratt RF]]
-	[[Category: Pratt~~, R F~~]]	+	[[Category: Silvaggi NR]]
-	[[Category: Silvaggi~~, N R]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Penicillin binding protein]]~~	+
-	~~[[Category: Peptidoglycan]]~~	+
-	~~[[Category: Products complex~~]]	+

OCA at 05:50, 28 April 2021

2021-04-28T05:50:11Z

←Older revision		Revision as of 05:50, 28 April 2021
Line 3:		Line 3:
	<StructureSection load='1iki' size='340' side='right'caption='[[1iki]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1iki' size='340' side='right'caption='[[1iki]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1IKI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IKI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REY:GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE'>REY</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REY:GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE'>REY</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ikg\|1ikg]], [[1hvb\|1hvb]], [[3pte\|3pte]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ikg\|1ikg]], [[1hvb\|1hvb]], [[3pte\|3pte]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iki OCA], [~~http~~://pdbe.org/1iki PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1iki RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1iki PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1iki 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=1iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iki OCA], [https://pdbe.org/1iki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iki RCSB], [https://www.ebi.ac.uk/pdbsum/1iki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iki ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DAC_STRSR DAC_STRSR]] Catalyzes distinct carboxypeptidation and transpeptidation reactions during the last stages of wall peptidoglycan synthesis. Mistaking a beta-lactam antibiotic molecule for a normal substrate (i.e. a D-alanyl-D-alanine-terminated peptide), it becomes immobilized in the form of a long-lived, serine-ester-linked acyl enzyme and thus behave as penicillin-binding protein (PBP).	+	[[https://www.uniprot.org/uniprot/DAC_STRSR DAC_STRSR]] Catalyzes distinct carboxypeptidation and transpeptidation reactions during the last stages of wall peptidoglycan synthesis. Mistaking a beta-lactam antibiotic molecule for a normal substrate (i.e. a D-alanyl-D-alanine-terminated peptide), it becomes immobilized in the form of a long-lived, serine-ester-linked acyl enzyme and thus behave as penicillin-binding protein (PBP).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:47, 24 July 2019

2019-07-24T06:47:19Z

←Older revision		Revision as of 06:47, 24 July 2019
Line 1:		Line 1:

	==COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT==		==COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT==
-	<StructureSection load='1iki' size='340' side='right' caption='[[1iki]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='1iki' size='340' side='right'caption='[[1iki]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IKI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IKI FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1iki" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1iki" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carboxypeptidase 3D structures\|Carboxypeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Streptomyces sp]]		[[Category: Streptomyces sp]]

OCA at 09:30, 10 January 2018

2018-01-10T09:30:36Z

←Older revision		Revision as of 09:30, 10 January 2018
Line 1:		Line 1:
		+
	==COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT==		==COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT==
	<StructureSection load='1iki' size='340' side='right' caption='[[1iki]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1iki' size='340' side='right' caption='[[1iki]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Strsr Strsr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IKI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IKI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REY:GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE'>REY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REY:GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE'>REY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ikg\|1ikg]], [[1hvb\|1hvb]], [[3pte\|3pte]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ikg\|1ikg]], [[1hvb\|1hvb]], [[3pte\|3pte]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iki OCA], [http://pdbe.org/1iki PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iki RCSB], [http://www.ebi.ac.uk/pdbsum/1iki 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=1iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iki OCA], [http://pdbe.org/1iki PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iki RCSB], [http://www.ebi.ac.uk/pdbsum/1iki PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1iki ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/1iki_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/1iki_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1iki" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1iki" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Penicillin-binding protein\|Penicillin-binding protein]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: ~~Strsr~~]]	+	[[Category: Streptomyces sp]]
	[[Category: Anderson, J W]]		[[Category: Anderson, J W]]
	[[Category: Kelly, J A]]		[[Category: Kelly, J A]]

OCA at 03:29, 7 February 2016

2016-02-07T03:29:08Z

←Older revision		Revision as of 03:29, 7 February 2016
Line 18:		Line 18:
	<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=1iki ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:16, 9 September 2015

2015-09-09T21:16:36Z

←Older revision		Revision as of 21:16, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1iki' size='340' side='right' caption='[[1iki]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1iki' size='340' side='right' caption='[[1iki]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_sp. Streptomyces sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IKI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strsr Strsr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IKI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REY:GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE'>REY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REY:GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE'>REY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ikg\|1ikg]], [[1hvb\|1hvb]], [[3pte\|3pte]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ikg\|1ikg]], [[1hvb\|1hvb]], [[3pte\|3pte]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iki OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iki RCSB], [http://www.ebi.ac.uk/pdbsum/1iki 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=1iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iki OCA], [http://pdbe.org/1iki PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iki RCSB], [http://www.ebi.ac.uk/pdbsum/1iki PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1iki" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: ~~Streptomyces sp~~]]	+	[[Category: Strsr]]
	[[Category: Anderson, J W]]		[[Category: Anderson, J W]]
	[[Category: Kelly, J A]]		[[Category: Kelly, J A]]

OCA at 07:30, 24 December 2014

2014-12-24T07:30:23Z

←Older revision		Revision as of 07:30, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IKI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IKI FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REY:GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE'>REY</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REY:GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE'>REY</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ikg\|1ikg]], [[1hvb\|1hvb]], [[3pte\|3pte]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ikg\|1ikg]], [[1hvb\|1hvb]], [[3pte\|3pte]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iki OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iki RCSB], [http://www.ebi.ac.uk/pdbsum/1iki 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=1iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iki OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iki RCSB], [http://www.ebi.ac.uk/pdbsum/1iki PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DAC_STRSR DAC_STRSR]] Catalyzes distinct carboxypeptidation and transpeptidation reactions during the last stages of wall peptidoglycan synthesis. Mistaking a beta-lactam antibiotic molecule for a normal substrate (i.e. a D-alanyl-D-alanine-terminated peptide), it becomes immobilized in the form of a long-lived, serine-ester-linked acyl enzyme and thus behave as penicillin-binding protein (PBP).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: Streptomyces sp.]]	+	[[Category: Streptomyces sp]]
-	[[Category: Anderson, J W.]]	+	[[Category: Anderson, J W]]
-	[[Category: Kelly, J A.]]	+	[[Category: Kelly, J A]]
-	[[Category: Knox, J R.]]	+	[[Category: Knox, J R]]
-	[[Category: Mcdonough, M A.]]	+	[[Category: Mcdonough, M A]]
-	[[Category: Pratt, R F.]]	+	[[Category: Pratt, R F]]
-	[[Category: Silvaggi, N R.]]	+	[[Category: Silvaggi, N R]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Penicillin binding protein]]		[[Category: Penicillin binding protein]]
	[[Category: Peptidoglycan]]		[[Category: Peptidoglycan]]
	[[Category: Products complex]]		[[Category: Products complex]]

OCA at 08:58, 28 September 2014

2014-09-28T08:58:55Z

←Older revision		Revision as of 08:58, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1iki.~~png~~\|~~left~~\|200px]]	+	==COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT==
		+	<StructureSection load='1iki' size='340' side='right' caption='[[1iki]], [[Resolution\|resolution]] 1.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1iki]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IKI FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REY:GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE'>REY</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ikg\|1ikg]], [[1hvb\|1hvb]], [[3pte\|3pte]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iki OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iki RCSB], [http://www.ebi.ac.uk/pdbsum/1iki 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/ik/1iki_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 ==
		+	Penicillin-binding proteins (PBPs), the target enzymes of beta-lactam antibiotics such as penicillins and cephalosporins, catalyze the final peptidoglycan cross-linking step of bacterial cell-wall biosynthesis. beta-Lactams inhibit this reaction because they mimic the D-alanyl-D-alanine peptide precursors of cell-wall structure. Prior crystallographic studies have described the site of beta-lactam binding and inhibition, but they have failed to show the binding of D-Ala-D-Ala substrates. We present here the first high-resolution crystallographic structures of a PBP, D-Ala-D-Ala-peptidase of Streptomyces sp. strain R61, non-covalently complexed with a highly specific fragment (glycyl-L-alpha-amino-epsilon-pimelyl-D-Ala-D-Ala) of the cell-wall precursor in both enzyme-substrate and enzyme-product forms. The 1.9A resolution structure of the enzyme-substrate Henri-Michaelis complex was achieved by using inactivated enzyme, which was formed by cross-linking two catalytically important residues Tyr159 and Lys65. The second structure at 1.25A resolution of the uncross-linked, active form of the DD-peptidase shows the non-covalent binding of the two products of the carboxypeptidase reaction. The well-defined substrate-binding site in the two crystallographic structures shows a subsite that is complementary to a portion of the natural cell-wall substrate that varies among bacterial species. In addition, the structures show the displacement of 11 water molecules from the active site, the location of residues responsible for substrate binding, and clearly demonstrate the necessity of Lys65 and or Tyr159 for the acylation step with the donor peptide. Comparison of the complexed structures described here with the structures of other known PBPs suggests the design of species-targeted antibiotics as a counter-strategy towards beta-lactamase-elicited bacterial resistance.

-	~~{{STRUCTURE_1iki\| PDB=1iki \| SCENE= }}~~	+	Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins.,McDonough MA, Anderson JW, Silvaggi NR, Pratt RF, Knox JR, Kelly JA J Mol Biol. 2002 Sep 6;322(1):111-22. PMID:12215418<ref>PMID:12215418</ref>

-	~~===COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12215418}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1iki]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Streptomyces_sp~~. ~~Streptomyces sp.]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA].~~	+

	==See Also==		==See Also==
-	*[[Carboxypeptidase\|Carboxypeptidase]]
	*[[Penicillin-binding protein\|Penicillin-binding protein]]		*[[Penicillin-binding protein\|Penicillin-binding protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012215418<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Streptomyces sp.]]		[[Category: Streptomyces sp.]]

OCA at 05:28, 20 October 2012

2012-10-20T05:28:18Z

←Older revision		Revision as of 05:28, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1iki]] is a 1 chain structure ~~of [[Carboxypeptidase]] and [[Penicillin-binding protein]]~~ with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA].	+	[[1iki]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKI OCA].

	==See Also==		==See Also==

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

2012-07-25T10:08:17Z

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

←Older revision

Revision as of 10:08, 25 July 2012