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| | ==Xaa-Pro peptidase from Deinococcus radiodurans, Zinc bound== | | ==Xaa-Pro peptidase from Deinococcus radiodurans, Zinc bound== |
| - | <StructureSection load='5giq' size='340' side='right' caption='[[5giq]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='5giq' size='340' side='right'caption='[[5giq]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5giq]] 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=5GIQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GIQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5giq]] 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=5GIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GIQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5cdv|5cdv]], [[5cdl|5cdl]], [[5giu|5giu]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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_1246 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</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=5giq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5giq OCA], [https://pdbe.org/5giq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5giq RCSB], [https://www.ebi.ac.uk/pdbsum/5giq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5giq 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=5giq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5giq OCA], [http://pdbe.org/5giq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5giq RCSB], [http://www.ebi.ac.uk/pdbsum/5giq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5giq ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q9RUY4_DEIRA Q9RUY4_DEIRA] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Deira]] | + | [[Category: Deinococcus radiodurans R1]] |
| - | [[Category: Are, V N]] | + | [[Category: Large Structures]] |
| - | [[Category: Ghosh, B]] | + | [[Category: Are VN]] |
| - | [[Category: Jamdar, S N]] | + | [[Category: Ghosh B]] |
| - | [[Category: Kumar, A]] | + | [[Category: Jamdar SN]] |
| - | [[Category: Makde, R D]] | + | [[Category: Kumar A]] |
| - | [[Category: Singh, R]] | + | [[Category: Makde RD]] |
| - | [[Category: Hydrolase]]
| + | [[Category: Singh R]] |
| - | [[Category: M24b fold]]
| + | |
| - | [[Category: Proline-specific]]
| + | |
| - | [[Category: Xaa-pro peptidase]]
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| Structural highlights
Function
Q9RUY4_DEIRA
Publication Abstract from PubMed
M24B peptidases cleaving Xaa-Pro bond in dipeptides are prolidases whereas those cleaving this bond in longer peptides are aminopeptidases-P. Bacteria have small aminopeptidases-P (36-39 kDa), which are diverged from canonical aminopeptidase-P of Escherichia coli (50 kDa). Structure-function studies of small aminopeptidases-P are lacking. We report crystal structures of small aminopeptidases-P from E. coli and Deinococcus radiodurans, and report substrate-specificities of these proteins and their ortholog from Mycobacterium tuberculosis. These are aminopeptidases-P, structurally close to small prolidases except for absence of dipeptide-selectivity loop. We noticed absence of this loop and conserved arginine in canonical archaeal prolidase (Maher et al., Biochemistry. 43, 2004, 2771-2783) and questioned its classification. Our enzymatic assays show that this enzyme is an aminopeptidase-P. Further, our mutagenesis studies illuminate importance of DXRY sequence motif in bacterial small aminopeptidases-P and suggest common evolutionary origin with human XPNPEP1/XPNPEP2. Our analyses reveal sequence/structural features distinguishing small aminopeptidases-P from other M24B peptidases.
Structures and activities of widely conserved small prokaryotic aminopeptidases-P clarify classification of M24B peptidases.,Are VN, Kumar A, Goyal VD, Gotad SS, Ghosh B, Gadre R, Jamdar SN, Makde RD Proteins. 2018 Dec 11. doi: 10.1002/prot.25641. PMID:30536999[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Are VN, Kumar A, Goyal VD, Gotad SS, Ghosh B, Gadre R, Jamdar SN, Makde RD. Structures and activities of widely conserved small prokaryotic aminopeptidases-P clarify classification of M24B peptidases. Proteins. 2018 Dec 11. doi: 10.1002/prot.25641. PMID:30536999 doi:http://dx.doi.org/10.1002/prot.25641
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