4y02: Difference between revisions

Revision as of 18:00, 26 April 2023

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

Structural highlights

4y02 is a 1 chain structure with sequence from Porphyromonas gingivalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	GOL, K
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPP11_PORG3 Catalyzes the removal of dipeptides from the N-terminus of oligopeptides. Shows a strict specificity for acidic residues (Asp or Glu) in the P1 position, and has a hydrophobic residue preference at the P2 position. Preferentially cleaves the synthetic substrate Leu-Asp-methylcoumaryl-7-amide (Leu-Asp-MCA) as compared to Leu-Glu-MCA. Is involved in amino acid metabolism and bacterial growth of asaccharolytic P.gingivalis, that utilizes amino acids from extracellular proteinaceous nutrients as energy and carbon sources.^[1] ^[2]

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^[3]

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

References

↑ Ohara-Nemoto Y, Shimoyama Y, Kimura S, Kon A, Haraga H, Ono T, Nemoto TK. Asp- and Glu-specific novel dipeptidyl peptidase 11 of Porphyromonas gingivalis ensures utilization of proteinaceous energy sources. J Biol Chem. 2011 Nov 4;286(44):38115-27. doi: 10.1074/jbc.M111.278572. Epub 2011, Sep 6. PMID:21896480 doi:https://dx.doi.org/10.1074/jbc.M111.278572
↑ Rouf SM, Ohara-Nemoto Y, Hoshino T, Fujiwara T, Ono T, Nemoto TK. Discrimination based on Gly and Arg/Ser at position 673 between dipeptidyl-peptidase (DPP) 7 and DPP11, widely distributed DPPs in pathogenic and environmental gram-negative bacteria. Biochimie. 2013 Apr;95(4):824-32. doi: 10.1016/j.biochi.2012.11.019. Epub 2012, Dec 12. PMID:23246913 doi:https://dx.doi.org/10.1016/j.biochi.2012.11.019
↑ 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

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Ohara-Nemoto Y, Shimoyama Y, Kimura S, Kon A, Haraga H, Ono T, Nemoto TK. Asp- and Glu-specific novel dipeptidyl peptidase 11 of Porphyromonas gingivalis ensures utilization of proteinaceous energy sources. J Biol Chem. 2011 Nov 4;286(44):38115-27. doi: 10.1074/jbc.M111.278572. Epub 2011, Sep 6. PMID:21896480 doi:https://dx.doi.org/10.1074/jbc.M111.278572

[2] Rouf SM, Ohara-Nemoto Y, Hoshino T, Fujiwara T, Ono T, Nemoto TK. Discrimination based on Gly and Arg/Ser at position 673 between dipeptidyl-peptidase (DPP) 7 and DPP11, widely distributed DPPs in pathogenic and environmental gram-negative bacteria. Biochimie. 2013 Apr;95(4):824-32. doi: 10.1016/j.biochi.2012.11.019. Epub 2012, Dec 12. PMID:23246913 doi:https://dx.doi.org/10.1016/j.biochi.2012.11.019

[3] 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]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='4y02' size='340' side='right'caption='[[4y02]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4y02]] is a 1 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=4Y02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y02 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4y02]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y02 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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
+</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=K:POTASSIUM+ION'>K</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xzy|4xzy]], [[4y01|4y01]], [[4y04|4y04]], [[4y06|4y06]]</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=4y02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y02 OCA], [https://pdbe.org/4y02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y02 RCSB], [https://www.ebi.ac.uk/pdbsum/4y02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y02 ProSAT]</span></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=4y02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y02 OCA], [http://pdbe.org/4y02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y02 RCSB], [http://www.ebi.ac.uk/pdbsum/4y02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y02 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPP11_PORG3 DPP11_PORG3] Catalyzes the removal of dipeptides from the N-terminus of oligopeptides. Shows a strict specificity for acidic residues (Asp or Glu) in the P1 position, and has a hydrophobic residue preference at the P2 position. Preferentially cleaves the synthetic substrate Leu-Asp-methylcoumaryl-7-amide (Leu-Asp-MCA) as compared to Leu-Glu-MCA. Is involved in amino acid metabolism and bacterial growth of asaccharolytic P.gingivalis, that utilizes amino acids from extracellular proteinaceous nutrients as energy and carbon sources.<ref>PMID:21896480</ref> <ref>PMID:23246913</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 33277]]
 [[Category: Large Structures]]
-[[Category: Fujimoto, M]]
+[[Category: Porphyromonas gingivalis]]
-[[Category: Iizuka, I]]
+[[Category: Fujimoto M]]
-[[Category: Nonaka, T]]
+[[Category: Iizuka I]]
-[[Category: Ogasawara, W]]
+[[Category: Nonaka T]]
-[[Category: Roppongi, S]]
+[[Category: Ogasawara W]]
-[[Category: Sakamoto, Y]]
+[[Category: Roppongi S]]
-[[Category: Suzuki, Y]]
+[[Category: Sakamoto Y]]
-[[Category: Tanaka, N]]
+[[Category: Suzuki Y]]
-[[Category: Tateoka, C]]
+[[Category: Tanaka N]]
-[[Category: Ground]]
+[[Category: Tateoka C]]
-[[Category: Hydrolase]]
-[[Category: Wt]]

4y02: Difference between revisions

Revision as of 18:00, 26 April 2023

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

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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