5xev - Revision history

OCA at 10:18, 27 March 2024

2024-03-27T10:18:10Z

←Older revision		Revision as of 10:18, 27 March 2024
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	==Crystal Structure of a novel Xaa-Pro dipeptidase from Deinococcus radiodurans==		==Crystal Structure of a novel Xaa-Pro dipeptidase from Deinococcus radiodurans==
-	<StructureSection load='5xev' size='340' side='right' caption='[[5xev]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='5xev' size='340' side='right'caption='[[5xev]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xev]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Deira Deira~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XEV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xev]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XEV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.4Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR_0478 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </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=5xev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xev OCA], [https://pdbe.org/5xev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xev RCSB], [https://www.ebi.ac.uk/pdbsum/5xev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xev ProSAT]</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=5xev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xev OCA], [~~http~~://pdbe.org/5xev PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xev RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xev PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xev ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9RX37_DEIRA Q9RX37_DEIRA]
-	Xaa-Pro peptidases (XPP) are dinuclear peptidases of MEROPS M24B family that hydrolyze Xaa-Pro iminopeptide bond with a trans-proline at the second position of the peptide substrate. XPPs specific towards dipeptides are called prolidases while those that prefer longer oligopeptides are called aminopeptidases P. Though XPPs are strictly conserved in bacterial and archaeal species, the structural and sequence features that distinguish between prolidases and aminopeptidases P are not always clear. Here, we report 1.4 A resolution crystal structure of a novel XPP from Deinococcus radiodurans (XPPdr). XPPdr forms a novel dimeric structure via unique dimer stabilization loops of N-terminal domains such that their C-terminal domains are placed far apart from each other. This novel dimerization is also the consequence of a different orientation of N-terminal domain in XPPdr monomer than those in other known prolidases. The enzymatic assays show that it is a prolidase with broad substrate specificity. Our structural, mutational, and molecular dynamics simulation analyses show that the conserved Arg46 of N-terminal domain is important for the dipeptide selectivity. Our BLAST search found XPPdr orthologs with conserved sequence motifs which correspond to unique structural features of XPPdr, thus identify a new subfamily of bacterial prolidases.	+
-		+
-	Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases.,Are VN, Jamdar SN, Ghosh B, Goyal VD, Kumar A, Neema S, Gadre R, Makde RD Proteins. 2017 Sep 20. doi: ~~10.1002~~/~~prot.25389. PMID:28929533<ref>PMID:28929533<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5xev" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deira~~]]	+	[[Category: Deinococcus radiodurans R1]]
-	[[Category: ~~Xaa-Pro dipeptidase~~]]	+	[[Category: Large Structures]]
-	[[Category: Are~~, V N~~]]	+	[[Category: Are VN]]
-	[[Category: Ghosh, B]]	+	[[Category: Ghosh B]]
-	[[Category: Kumar, A]]	+	[[Category: Kumar A]]
-	[[Category: Makde~~, R D]]~~	+	[[Category: Makde RD]]
-	~~[[Category: Deinococcus radioduran]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: M28b peptidase]]~~	+
-	~~[[Category: Prolidase]]~~	+
-	~~[[Category: Xaa-pro dipeptidase~~]]	+

OCA at 07:41, 29 November 2017

2017-11-29T07:41:28Z

←Older revision		Revision as of 07:41, 29 November 2017
Line 3:		Line 3:
	<StructureSection load='5xev' size='340' side='right' caption='[[5xev]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5xev' size='340' side='right' caption='[[5xev]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xev]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XEV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xev]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XEV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR_0478 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </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=5xev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xev OCA], [http://pdbe.org/5xev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xev RCSB], [http://www.ebi.ac.uk/pdbsum/5xev PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xev ProSAT]</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=5xev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xev OCA], [http://pdbe.org/5xev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xev RCSB], [http://www.ebi.ac.uk/pdbsum/5xev PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xev ProSAT]</span></td></tr>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deira]]
	[[Category: Xaa-Pro dipeptidase]]		[[Category: Xaa-Pro dipeptidase]]
	[[Category: Are, V N]]		[[Category: Are, V N]]

OCA at 07:02, 18 October 2017

2017-10-18T07:02:29Z

←Older revision		Revision as of 07:02, 18 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xev is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of a novel Xaa-Pro dipeptidase from Deinococcus radiodurans==
		+	<StructureSection load='5xev' size='340' side='right' caption='[[5xev]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xev]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XEV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </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=5xev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xev OCA], [http://pdbe.org/5xev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xev RCSB], [http://www.ebi.ac.uk/pdbsum/5xev PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xev ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Xaa-Pro peptidases (XPP) are dinuclear peptidases of MEROPS M24B family that hydrolyze Xaa-Pro iminopeptide bond with a trans-proline at the second position of the peptide substrate. XPPs specific towards dipeptides are called prolidases while those that prefer longer oligopeptides are called aminopeptidases P. Though XPPs are strictly conserved in bacterial and archaeal species, the structural and sequence features that distinguish between prolidases and aminopeptidases P are not always clear. Here, we report 1.4 A resolution crystal structure of a novel XPP from Deinococcus radiodurans (XPPdr). XPPdr forms a novel dimeric structure via unique dimer stabilization loops of N-terminal domains such that their C-terminal domains are placed far apart from each other. This novel dimerization is also the consequence of a different orientation of N-terminal domain in XPPdr monomer than those in other known prolidases. The enzymatic assays show that it is a prolidase with broad substrate specificity. Our structural, mutational, and molecular dynamics simulation analyses show that the conserved Arg46 of N-terminal domain is important for the dipeptide selectivity. Our BLAST search found XPPdr orthologs with conserved sequence motifs which correspond to unique structural features of XPPdr, thus identify a new subfamily of bacterial prolidases.

-	~~Authors~~:	+	Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases.,Are VN, Jamdar SN, Ghosh B, Goyal VD, Kumar A, Neema S, Gadre R, Makde RD Proteins. 2017 Sep 20. doi: 10.1002/prot.25389. PMID:28929533<ref>PMID:28929533</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xev" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Xaa-Pro dipeptidase]]
		+	[[Category: Are, V N]]
		+	[[Category: Ghosh, B]]
		+	[[Category: Kumar, A]]
		+	[[Category: Makde, R D]]
		+	[[Category: Deinococcus radioduran]]
		+	[[Category: Hydrolase]]
		+	[[Category: M28b peptidase]]
		+	[[Category: Prolidase]]
		+	[[Category: Xaa-pro dipeptidase]]

OCA at 12:59, 27 April 2017

2017-04-27T12:59:40Z

←Older revision		Revision as of 12:59, 27 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xev is ON HOLD	+	The entry 5xev is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5xev" [edit=sysop:move=sysop]

2017-04-12T10:42:29Z

Protected "5xev" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:42, 12 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xev is ON HOLD Authors: Description: Category: Unreleased Structures

2017-04-12T10:42:28Z

New page: '''Unreleased structure''' The entry 5xev is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xev is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]