5sdp: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
m Protected "5sdp" [edit=sysop:move=sysop]
No edit summary
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
'''Unreleased structure'''


The entry 5sdp is ON HOLD
==PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z2277255954==
<StructureSection load='5sdp' size='340' side='right'caption='[[5sdp]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5sdp]] 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=5SDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SDP FirstGlance]. <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]] 2.195&#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=I8J:5-fluoro-1-(1-methylcyclopropane-1-sulfonyl)-1,2,3,6-tetrahydropyridine'>I8J</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=5sdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sdp OCA], [https://pdbe.org/5sdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sdp RCSB], [https://www.ebi.ac.uk/pdbsum/5sdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sdp 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>


Authors: Tham, C.T., Coker, J.A., Krojer, T., Foster, W.R., Koekemoer, L., Douangamath, A., Talon, R., Fearon, D., von Delft, F., Yue, W.W., Bountra, C., Bezerra, G.A.
==See Also==
 
*[[Dipeptidyl peptidase 3D structures|Dipeptidyl peptidase 3D structures]]
Description: PanDDA analysis group deposition --Crystal Structure of Porphyromonas gingivalis in complex with Z2277255954
== References ==
[[Category: Unreleased Structures]]
<references/>
[[Category: Foster, W.R]]
__TOC__
[[Category: Talon, R]]
</StructureSection>
[[Category: Bezerra, G.A]]
[[Category: Large Structures]]
[[Category: Douangamath, A]]
[[Category: Porphyromonas gingivalis]]
[[Category: Fearon, D]]
[[Category: Bezerra GA]]
[[Category: Krojer, T]]
[[Category: Bountra C]]
[[Category: Yue, W.W]]
[[Category: Coker JA]]
[[Category: Coker, J.A]]
[[Category: Douangamath A]]
[[Category: Tham, C.T]]
[[Category: Fearon D]]
[[Category: Von Delft, F]]
[[Category: Foster WR]]
[[Category: Bountra, C]]
[[Category: Koekemoer L]]
[[Category: Koekemoer, L]]
[[Category: Krojer T]]
[[Category: Talon R]]
[[Category: Tham CT]]
[[Category: Yue WW]]
[[Category: Von Delft F]]

Latest revision as of 18:31, 6 March 2024

PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z2277255954PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z2277255954

Structural highlights

5sdp 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 2.195Å
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

5sdp, resolution 2.19Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=5sdp&oldid=4084601"