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| | <StructureSection load='6a4t' size='340' side='right'caption='[[6a4t]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='6a4t' size='340' side='right'caption='[[6a4t]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6a4t]] is a 2 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=6A4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A4T FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6a4t]] is a 2 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=6A4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A4T FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_1070 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</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]] 2Å</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=6a4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4t OCA], [http://pdbe.org/6a4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a4t RCSB], [http://www.ebi.ac.uk/pdbsum/6a4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4t ProSAT]</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=6a4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4t OCA], [https://pdbe.org/6a4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a4t RCSB], [https://www.ebi.ac.uk/pdbsum/6a4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4t ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Y1070_DEIRA Y1070_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: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Gokhale, S M]] | + | [[Category: Gokhale SM]] |
| - | [[Category: Goyal, V G]] | + | [[Category: Goyal VG]] |
| - | [[Category: Kumar, A]] | + | [[Category: Kumar A]] |
| - | [[Category: Makde, R D]] | + | [[Category: Makde RD]] |
| - | [[Category: Yadav, P]] | + | [[Category: Yadav P]] |
| - | [[Category: Active site]]
| + | |
| - | [[Category: Dimer]]
| + | |
| - | [[Category: Esterase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Peptidase e]]
| + | |
| - | [[Category: S51 peptidase]]
| + | |
| Structural highlights
Function
Y1070_DEIRA
Publication Abstract from PubMed
Peptidase E (PepE) is a nonclassical serine peptidase with a Ser-His-Glu catalytic triad. It is specific for dipeptides with an N-terminal aspartate residue (Asp-X dipeptidase activity). Its homolog from Listeria monocytogenes (PepElm) has a Ser-His-Asn "catalytic triad." Based on sequence alignment we predicted that the PepE homolog from Deinococcus radiodurans (PepEdr) would have a Ser-His-Asp "catalytic triad." We confirmed this by solving the crystal structure of PepEdr to 2.7 A resolution. We show that PepElm and PepEdr lack the Asp-X dipeptidase activity. Our analyses suggest that absence of P1 pocket in the active site could be the main reason for this lack of typical activity. Sequence and structural data reveal that the PepE homologs can be divided into long and short PepEs based on presence or absence of a C-terminal tail which adopts a beta-hairpin conformation in the canonical PepE from Salmonella enterica. A long PepE from Bacillus subtilis with Ser-His-Asp catalytic triad exhibits Asp-X dipeptidase activity. Whereas the three long PepEs enzymatically characterized till date have been found to possess the Asp-X dipeptidase activity, the three enzymatically characterized short PepEs lack this activity irrespective of the nature of their catalytic triads. This study illuminates the structural and functional heterogeneity in the S51 family and also provides structural basis for the functional variability among PepE homologs.
Catalytic triad heterogeneity in S51 peptidase family: Structural basis for functional variability.,Yadav P, Goyal VD, Chandravanshi K, Kumar A, Gokhale SM, Jamdar SN, Makde RD Proteins. 2019 Aug;87(8):679-692. doi: 10.1002/prot.25693. Epub 2019 May 3. PMID:30968972[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yadav P, Goyal VD, Chandravanshi K, Kumar A, Gokhale SM, Jamdar SN, Makde RD. Catalytic triad heterogeneity in S51 peptidase family: Structural basis for functional variability. Proteins. 2019 Aug;87(8):679-692. doi: 10.1002/prot.25693. Epub 2019 May 3. PMID:30968972 doi:http://dx.doi.org/10.1002/prot.25693
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