4y01: Difference between revisions

Revision as of 23:36, 5 June 2019

Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis

Structural highlights

4y01 is a 2 chain structure with sequence from Atcc 33277. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	GOL
NonStd Res:	MSE
Related:	4xzy, 4y02, 4y04, 4y06
Gene:	EG14_04230 (ATCC 33277)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to the S46 family of serine peptidases and preferentially cleaves substrates with Asp/Glu at the P1 position. The molecular mechanism underlying the substrate specificity of PgDPP11, however, is unknown. Here, we report the crystal structure of PgDPP11. The enzyme contains a catalytic domain with a typical double beta-barrel fold and a recently identified regulatory alpha-helical domain. Crystal structure analyses, docking studies, and biochemical studies revealed that the side chain of Arg673 in the S1 subsite is essential for recognition of the Asp/Glu side chain at the P1 position of the bound substrate. Because S46 peptidases are not found in mammals and the Arg673 is conserved among DPP11s, we anticipate that DPP11s could be utilised as targets for antibiotics. In addition, the present structure analyses could be useful templates for the design of specific inhibitors of DPP11s from pathogenic organisms.

Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity.,Sakamoto Y, Suzuki Y, Iizuka I, Tateoka C, Roppongi S, Fujimoto M, Inaka K, Tanaka H, Yamada M, Ohta K, Gouda H, Nonaka T, Ogasawara W, Tanaka N Sci Rep. 2015 Jun 9;5:11151. doi: 10.1038/srep11151. PMID:26057589^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sakamoto Y, Suzuki Y, Iizuka I, Tateoka C, Roppongi S, Fujimoto M, Inaka K, Tanaka H, Yamada M, Ohta K, Gouda H, Nonaka T, Ogasawara W, Tanaka N. Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity. Sci Rep. 2015 Jun 9;5:11151. doi: 10.1038/srep11151. PMID:26057589 doi:https://dx.doi.org/10.1038/srep11151

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OCA

[1] Sakamoto Y, Suzuki Y, Iizuka I, Tateoka C, Roppongi S, Fujimoto M, Inaka K, Tanaka H, Yamada M, Ohta K, Gouda H, Nonaka T, Ogasawara W, Tanaka N. Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity. Sci Rep. 2015 Jun 9;5:11151. doi: 10.1038/srep11151. PMID:26057589 doi:https://dx.doi.org/10.1038/srep11151

[1]

@@ Line 1: / Line 1: @@
 ==Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis==
-<StructureSection load='4y01' size='340' side='right' caption='[[4y01]], [[Resolution|resolution]] 2.46&Aring;' scene=''>
+<StructureSection load='4y01' size='340' side='right'caption='[[4y01]], [[Resolution|resolution]] 2.46&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4y01]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y01 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4y01]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33277 Atcc 33277]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y01 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></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xzy|4xzy]], [[4y02|4y02]], [[4y04|4y04]], [[4y06|4y06]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EG14_04230 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=837 ATCC 33277])</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=4y01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y01 OCA], [http://pdbe.org/4y01 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y01 RCSB], [http://www.ebi.ac.uk/pdbsum/4y01 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y01 ProSAT]</span></td></tr>
 </table>
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 4y01" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dipeptidyl peptidase|Dipeptidyl peptidase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Atcc 33277]]
+[[Category: Large Structures]]
 [[Category: Fujimoto, M]]
 [[Category: Iizuka, I]]

4y01: Difference between revisions

Revision as of 23:36, 5 June 2019

Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis

Structural highlights

Publication Abstract from PubMed

See Also

References

Contents

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