5sdl: Difference between revisions

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==PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z321318226==
==PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z321318226==
<StructureSection load='5sdl' size='340' side='right'caption='[[5sdl]]' scene=''>
<StructureSection load='5sdl' size='340' side='right'caption='[[5sdl]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SDL FirstGlance]. <br>
<table><tr><td colspan='2'>[[5sdl]] is a 2 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=5SDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SDL FirstGlance]. <br>
</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=5sdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sdl OCA], [https://pdbe.org/5sdl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sdl RCSB], [https://www.ebi.ac.uk/pdbsum/5sdl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sdl ProSAT]</span></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]] 2.44&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=JHJ:N-(4-methoxyphenyl)-N-pyridin-4-ylurea'>JHJ</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=5sdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sdl OCA], [https://pdbe.org/5sdl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sdl RCSB], [https://www.ebi.ac.uk/pdbsum/5sdl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sdl ProSAT]</span></td></tr>
</table>
</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>
==See Also==
*[[Dipeptidyl peptidase 3D structures|Dipeptidyl peptidase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Porphyromonas gingivalis]]
[[Category: Bezerra GA]]
[[Category: Bezerra GA]]
[[Category: Bountra C]]
[[Category: Bountra C]]

Revision as of 18:31, 6 March 2024

PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z321318226PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z321318226

Structural highlights

5sdl is a 2 chain structure with sequence from Porphyromonas gingivalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.44Å
Ligands:,
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]

See Also

References

  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:http://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:http://dx.doi.org/10.1016/j.biochi.2012.11.019

5sdl, resolution 2.44Å

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