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3wol

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Crystal structure of the DAP BII dipeptide complex I

Structural highlights

3wol 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 1.74Å
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 aminopeptidase BII (DAP BII) belongs to a serine peptidase family, S46. The amino acid sequence of the catalytic unit of DAP BII exhibits significant similarity to those of clan PA endopeptidases, such as chymotrypsin. However, the molecular mechanism of the exopeptidase activity of family S46 peptidase is unknown. Here, we report crystal structures of DAP BII. DAP BII contains a peptidase domain including a typical double beta-barrel fold and previously unreported alpha-helical domain. The structures of peptide complexes revealed that the alpha-helical domain covers the active-site cleft and the side chain of Asn330 in the domain forms hydrogen bonds with the N-terminus of the bound peptide. These observations indicate that the alpha-helical domain regulates the exopeptidase activity of DAP BII. Because S46 peptidases are not found in mammals, we expect that our study will be useful for the design of specific inhibitors of S46 peptidases from pathogens.

S46 peptidases are the first exopeptidases to be members of clan PA.,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 Sci Rep. 2014 May 15;4:4977. doi: 10.1038/srep04977. PMID:24827749^[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, 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

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/3wol"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the DAP BII dipeptide complex I==
-<StructureSection load='3wol' size='340' side='right' caption='[[3wol]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
+<StructureSection load='3wol' size='340' side='right'caption='[[3wol]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3wol]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WOL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3wol]] 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=3WOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WOL FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.74&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3woi|3woi]], [[3woj|3woj]], [[3wok|3wok]], [[3wom|3wom]], [[3won|3won]], [[3woo|3woo]], [[3wop|3wop]], [[3woq|3woq]], [[3wor|3wor]]</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=TYR:TYROSINE'>TYR</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wol OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wol RCSB], [http://www.ebi.ac.uk/pdbsum/3wol PDBsum]</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=3wol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wol OCA], [https://pdbe.org/3wol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wol RCSB], [https://www.ebi.ac.uk/pdbsum/3wol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wol ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DAPB2_PSEMX 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).<ref>PMID:24598890</ref> <ref>PMID:24827749</ref> <ref>PMID:8892831</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 15: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3wol" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Fujimoto, M.]]
+[[Category: Large Structures]]
-[[Category: Iizuka, I.]]
+[[Category: Pseudoxanthomonas mexicana]]
-[[Category: Nonaka, T.]]
+[[Category: Fujimoto M]]
-[[Category: Ogasawara, W.]]
+[[Category: Iizuka I]]
-[[Category: Roppongi, S.]]
+[[Category: Nonaka T]]
-[[Category: Sakamoto, Y.]]
+[[Category: Ogasawara W]]
-[[Category: Suzuki, Y.]]
+[[Category: Roppongi S]]
-[[Category: Tanaka, N.]]
+[[Category: Sakamoto Y]]
-[[Category: Tateoka, C.]]
+[[Category: Suzuki Y]]
-[[Category: Chymotrypsin fold]]
+[[Category: Tanaka N]]
-[[Category: Hydrolase]]
+[[Category: Tateoka C]]
-[[Category: S46 peptidase]]

3wol

From Proteopedia

Current revision

Crystal structure of the DAP BII dipeptide complex I

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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