5fcf - Revision history

OCA at 09:11, 20 March 2024

2024-03-20T09:11:58Z

←Older revision		Revision as of 09:11, 20 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q8P839_XANCP Q8P839_XANCP]		[https://www.uniprot.org/uniprot/Q8P839_XANCP Q8P839_XANCP]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Xaa-Pro dipeptidase (XPD) catalyzes hydrolysis of iminopeptide bond in dipeptides containing trans-proline as a second residue. XPDs are found in all living organisms and are believed to play an essential role in proline metabolism. Here, we report crystal structures and extensive enzymatic studies of XPD from Xanthomonas campestris (XPDxc), the first such comprehensive study of a bacterial XPD. We also report enzymatic activities of its ortholog from Mycobacterium tuberculosis (XPDmt). These enzymes are strictly dipeptidases with broad substrate specificities. They exhibit substrate inhibition and allostericity, as described earlier for XPD from Lactococcus lactis (XPDll). The structural, mutational and comparative data have revealed a novel mechanism of dipeptide selectivity and substrate binding in these enzymes. Moreover, we have identified conserved sequence motifs that distinguish these enzymes from other prolidases, thus defining a new subfamily. This study provides a suitable structural template for explaining unique properties of this XPDxc subfamily. In addition, we report unique structural features of XPDxc protein like an extended N-terminal tail region and absence of a conserved Tyr residue near the active site.
-
-	Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro dipeptidases.,Are VN, Kumar A, Kumar S, Goyal VD, Ghosh B, Bhatnagar D, Jamdar SN, Makde RD Biochim Biophys Acta. 2016 Nov 2;1865(2):153-164. doi:, 10.1016/j.bbapap.2016.10.016. PMID:27816563<ref>PMID:27816563</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5fcf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Serine/threonine protein kinase 3D structures\|Serine/threonine protein kinase 3D structures]]		*[[Serine/threonine protein kinase 3D structures\|Serine/threonine protein kinase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:46, 19 July 2023

2023-07-19T06:46:13Z

←Older revision		Revision as of 06:46, 19 July 2023
Line 3:		Line 3:
	<StructureSection load='5fcf' size='340' side='right'caption='[[5fcf]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5fcf' size='340' side='right'caption='[[5fcf]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fcf]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Xancp Xancp~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FCF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fcf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris_str._ATCC_33913 Xanthomonas campestris pv. campestris str. ATCC 33913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FCF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.85Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r60\|4r60]], [[5fch\|5fch]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pepQ, XCC2409 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190485 XANCP])</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=5fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fcf OCA], [https://pdbe.org/5fcf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fcf RCSB], [https://www.ebi.ac.uk/pdbsum/5fcf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fcf ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/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~~://proteopedia.org/fgij/fg.htm?mol=5fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fcf OCA], [~~http~~://pdbe.org/5fcf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fcf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fcf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fcf ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8P839_XANCP Q8P839_XANCP]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Xaa-Pro dipeptidase]]~~	+	[[Category: Xanthomonas campestris pv. campestris str. ATCC 33913]]
-	~~[[Category: Xancp~~]]	+	[[Category: Are V]]
-	[[Category: Are, V]]	+	[[Category: Ghosh B]]
-	[[Category: Ghosh, B]]	+	[[Category: Jamdar S]]
-	[[Category: Jamdar, S]]	+	[[Category: Kumar A]]
-	[[Category: Kumar, A]]	+	[[Category: Makde RD]]
-	[[Category: Makde~~, R D]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: M24 family]]~~	+
-	~~[[Category: Phosphate]]~~	+
-	~~[[Category: Prolidase]]~~	+
-	~~[[Category: Xaa-pro dipeptidase~~]]	+

OCA at 08:10, 29 April 2020

2020-04-29T08:10:42Z

←Older revision		Revision as of 08:10, 29 April 2020
Line 1:		Line 1:

	==Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Mn bound==		==Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Mn bound==
-	<StructureSection load='5fcf' size='340' side='right' caption='[[5fcf]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5fcf' size='340' side='right'caption='[[5fcf]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fcf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FCF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fcf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Xancp Xancp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FCF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r60\|4r60]], [[5fch\|5fch]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r60\|4r60]], [[5fch\|5fch]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pepQ, XCC2409 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190485 XANCP])</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=5fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fcf OCA], [http://pdbe.org/5fcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fcf RCSB], [http://www.ebi.ac.uk/pdbsum/5fcf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fcf ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fcf OCA], [http://pdbe.org/5fcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fcf RCSB], [http://www.ebi.ac.uk/pdbsum/5fcf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fcf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5fcf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fcf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Serine/threonine protein kinase 3D structures\|Serine/threonine protein kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Xaa-Pro dipeptidase]]		[[Category: Xaa-Pro dipeptidase]]
		+	[[Category: Xancp]]
	[[Category: Are, V]]		[[Category: Are, V]]
	[[Category: Ghosh, B]]		[[Category: Ghosh, B]]

OCA at 19:36, 9 December 2016

2016-12-09T19:36:46Z

←Older revision		Revision as of 19:36, 9 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fcf is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Mn bound==
		+	<StructureSection load='5fcf' size='340' side='right' caption='[[5fcf]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fcf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FCF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r60\|4r60]], [[5fch\|5fch]]</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=5fcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fcf OCA], [http://pdbe.org/5fcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fcf RCSB], [http://www.ebi.ac.uk/pdbsum/5fcf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fcf ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Xaa-Pro dipeptidase (XPD) catalyzes hydrolysis of iminopeptide bond in dipeptides containing trans-proline as a second residue. XPDs are found in all living organisms and are believed to play an essential role in proline metabolism. Here, we report crystal structures and extensive enzymatic studies of XPD from Xanthomonas campestris (XPDxc), the first such comprehensive study of a bacterial XPD. We also report enzymatic activities of its ortholog from Mycobacterium tuberculosis (XPDmt). These enzymes are strictly dipeptidases with broad substrate specificities. They exhibit substrate inhibition and allostericity, as described earlier for XPD from Lactococcus lactis (XPDll). The structural, mutational and comparative data have revealed a novel mechanism of dipeptide selectivity and substrate binding in these enzymes. Moreover, we have identified conserved sequence motifs that distinguish these enzymes from other prolidases, thus defining a new subfamily. This study provides a suitable structural template for explaining unique properties of this XPDxc subfamily. In addition, we report unique structural features of XPDxc protein like an extended N-terminal tail region and absence of a conserved Tyr residue near the active site.

-	~~Authors: Kumar, A~~., Are, V., ~~Ghosh~~, B., Jamdar, S., ~~Makde, R~~.D.	+	Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro dipeptidases.,Are VN, Kumar A, Kumar S, Goyal VD, Ghosh B, Bhatnagar D, Jamdar SN, Makde RD Biochim Biophys Acta. 2016 Nov 2;1865(2):153-164. doi:, 10.1016/j.bbapap.2016.10.016. PMID:27816563<ref>PMID:27816563</ref>

-	~~Description: Crystal Structure~~ of ~~Xaa~~-~~Pro dipeptidase from Xanthomonas campestris, phosphate and Mn bound~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5fcf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Xaa-Pro dipeptidase]]
	[[Category: Are, V]]		[[Category: Are, V]]
-	[[Category: Kumar, A]]
-	[[Category: Jamdar, S]]
-	[[Category: Makde, R.D]]
	[[Category: Ghosh, B]]		[[Category: Ghosh, B]]
		+	[[Category: Jamdar, S]]
		+	[[Category: Kumar, A]]
		+	[[Category: Makde, R D]]
		+	[[Category: Hydrolase]]
		+	[[Category: M24 family]]
		+	[[Category: Phosphate]]
		+	[[Category: Prolidase]]
		+	[[Category: Xaa-pro dipeptidase]]

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

2015-12-23T11:26:55Z

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

←Older revision

Revision as of 11:26, 23 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fcf is ON HOLD until Paper Publication Authors: Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.D. Description: Crystal Structure of Xaa-Pro d...

2015-12-23T11:26:54Z

New page: '''Unreleased structure''' The entry 5fcf is ON HOLD until Paper Publication Authors: Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.D. Description: Crystal Structure of Xaa-Pro d...

New page

'''Unreleased structure'''

The entry 5fcf is ON HOLD until Paper Publication

Authors: Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.D.

Description: Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Mn bound
[[Category: Unreleased Structures]]
[[Category: Are, V]]
[[Category: Kumar, A]]
[[Category: Jamdar, S]]
[[Category: Makde, R.D]]
[[Category: Ghosh, B]]