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5xev

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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==
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<StructureSection load='5xev' size='340' side='right' caption='[[5xev]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
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<StructureSection load='5xev' size='340' side='right'caption='[[5xev]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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>
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<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>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
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<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>
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<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>
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<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>
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<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>
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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=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>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q9RX37_DEIRA Q9RX37_DEIRA]
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5xev" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Deira]]
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[[Category: Deinococcus radiodurans R1]]
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[[Category: Xaa-Pro dipeptidase]]
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[[Category: Large Structures]]
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[[Category: Are, V N]]
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[[Category: Are VN]]
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[[Category: Ghosh, B]]
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[[Category: Ghosh B]]
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[[Category: Kumar, A]]
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[[Category: Kumar A]]
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[[Category: Makde, R D]]
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[[Category: Makde RD]]
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[[Category: Deinococcus radioduran]]
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[[Category: Hydrolase]]
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[[Category: M28b peptidase]]
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[[Category: Prolidase]]
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[[Category: Xaa-pro dipeptidase]]
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Current revision

Crystal Structure of a novel Xaa-Pro dipeptidase from Deinococcus radiodurans

PDB ID 5xev

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