This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4y06

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of the DAP BII (G675R) dipeptide complex

Structural highlights

4y06 is a 2 chain structure with sequence from Pseudoxanthomonas mexicana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.18Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DAPB2_PSEMX Exopeptidase that catalyzes the removal of dipeptide units (NH2-P2-P1-) from the free amino termini of oligopeptides and small proteins (PubMed:24598890, PubMed:8892831, PubMed:24827749). Peptide digestion is sequential and substrate recognition is non-specific, with the exception that Pro is not suitable as a P1 residue (PubMed:24827749). Removes many residues of bioactive oligopeptides such as angiotensin I and neuromedin N and cleaves also oxidized insulin B chain. Able to hydrolyze an X-Pro bond, an imido bond. No endopeptidase activity (PubMed:8892831). May play a physiological role in feeding (PubMed:24598890).^[1] ^[2] ^[3]

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^[4]

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

References

↑ Suzuki Y, Sakamoto Y, Tanaka N, Okada H, Morikawa Y, Ogasawara W. Identification of the catalytic triad of family S46 exopeptidases, closely related to clan PA endopeptidases. Sci Rep. 2014 Mar 6;4:4292. PMID:24598890 doi:10.1038/srep04292
↑ Sakamoto Y, Suzuki Y, Iizuka I, Tateoka C, Roppongi S, Fujimoto M, Inaka K, Tanaka H, Masaki M, Ohta K, Okada H, Nonaka T, Morikawa Y, Nakamura KT, Ogasawara W, Tanaka N. S46 peptidases are the first exopeptidases to be members of clan PA. Sci Rep. 2014 May 15;4:4977. doi: 10.1038/srep04977. PMID:24827749 doi:http://dx.doi.org/10.1038/srep04977
↑ Ogasawara W, Kobayashi G, Okada H, Morikawa Y. Two types of novel dipeptidyl aminopeptidases from Pseudomonas sp. strain WO24. J Bacteriol. 1996 Nov;178(21):6288-95. PMID:8892831 doi:10.1128/jb.178.21.6288-6295.1996
↑ 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:http://dx.doi.org/10.1038/srep11151

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4y06"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4y06]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudoxanthomonas_mexicana Pseudoxanthomonas mexicana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y06 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</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]] 2.18&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4y06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y06 OCA], [https://pdbe.org/4y06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y06 RCSB], [https://www.ebi.ac.uk/pdbsum/4y06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y06 ProSAT]</span></td></tr>
 </table>

4y06

From Proteopedia

Current revision

Crystal structure of the DAP BII (G675R) dipeptide complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox