5fcf

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<StructureSection load='5fcf' size='340' side='right'caption='[[5fcf]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
<StructureSection load='5fcf' size='340' side='right'caption='[[5fcf]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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>
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<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>
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</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>
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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]] 1.85&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4r60|4r60]], [[5fch|5fch]]</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=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>
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<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>
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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=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>
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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'>[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>
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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/Q8P839_XANCP Q8P839_XANCP]
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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.
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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>
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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 5fcf" style="background-color:#fffaf0;"></div>
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==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]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Xaa-Pro dipeptidase]]
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[[Category: Xanthomonas campestris pv. campestris str. ATCC 33913]]
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[[Category: Xancp]]
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[[Category: Are V]]
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[[Category: Are, V]]
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[[Category: Ghosh B]]
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[[Category: Ghosh, B]]
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[[Category: Jamdar S]]
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[[Category: Jamdar, S]]
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[[Category: Kumar A]]
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[[Category: Kumar, A]]
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[[Category: Makde RD]]
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[[Category: Makde, R D]]
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[[Category: Hydrolase]]
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[[Category: M24 family]]
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[[Category: Phosphate]]
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[[Category: Prolidase]]
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[[Category: Xaa-pro dipeptidase]]
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Current revision

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Mn bound

PDB ID 5fcf

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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