2d5l: Difference between revisions
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[[Image:2d5l.gif|left|200px]] | [[Image:2d5l.gif|left|200px]] | ||
'''Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis''' | {{Structure | ||
|PDB= 2d5l |SIZE=350|CAPTION= <scene name='initialview01'>2d5l</scene>, resolution 2.10Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene> | |||
|ACTIVITY= | |||
|GENE= PG1361 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=837 Porphyromonas gingivalis]) | |||
}} | |||
'''Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2D5L is a [ | 2D5L is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D5L OCA]. | ||
==Reference== | ==Reference== | ||
Crystal structure and mechanism of tripeptidyl activity of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis., Ito K, Nakajima Y, Xu Y, Yamada N, Onohara Y, Ito T, Matsubara F, Kabashima T, Nakayama K, Yoshimoto T, J Mol Biol. 2006 Sep 15;362(2):228-40. Epub 2006 Aug 17. PMID:[http:// | Crystal structure and mechanism of tripeptidyl activity of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis., Ito K, Nakajima Y, Xu Y, Yamada N, Onohara Y, Ito T, Matsubara F, Kabashima T, Nakayama K, Yoshimoto T, J Mol Biol. 2006 Sep 15;362(2):228-40. Epub 2006 Aug 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16914159 16914159] | ||
[[Category: Porphyromonas gingivalis]] | [[Category: Porphyromonas gingivalis]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: serine peptidase]] | [[Category: serine peptidase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:23:37 2008'' | ||
Revision as of 17:23, 20 March 2008
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| , resolution 2.10Å | |||||||
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| Ligands: | |||||||
| Gene: | PG1361 (Porphyromonas gingivalis) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis
OverviewOverview
The crystal structure of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis was determined. Prolyl tripeptidyl aminopeptidase consists of beta-propeller and catalytic domains, and a large cavity between the domains; this structure is similar to dipeptidyl aminopeptidase IV. A catalytic triad (Ser603, His710, and Asp678) was located in the catalytic domain; this triad was virtually identical to that of the enzymes belonging to the prolyl oligopeptidase family. The structure of an inactive S603A mutant enzyme complexed with a substrate was also determined. The pyrrolidine ring of the proline residue appeared to fit into a hydrophobic pocket composed of Tyr604, Val629, Trp632, Tyr635, Tyr639, Val680, and Val681. There were characteristic differences in the residues of the beta-propeller domain, and these differences were related to the substrate specificity of tripeptidyl activity. The N-terminal amino group was recognized by salt bridges, with two carboxyl groups of Glu205 and Glu206 from a helix in dipeptidyl aminopeptidase IV. In prolyl tripeptidyl aminopeptidase, however, the Glu205 (located in the loop) and Glu636 were found to carry out this function. The loop structure provides sufficient space to accommodate three N-terminal residues (Xaa-Xaa-Pro) of substrates. This is the first report of the structure and substrate recognition mechanism of tripeptidyl peptidase.
About this StructureAbout this Structure
2D5L is a Single protein structure of sequence from Porphyromonas gingivalis. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structure and mechanism of tripeptidyl activity of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis., Ito K, Nakajima Y, Xu Y, Yamada N, Onohara Y, Ito T, Matsubara F, Kabashima T, Nakayama K, Yoshimoto T, J Mol Biol. 2006 Sep 15;362(2):228-40. Epub 2006 Aug 17. PMID:16914159
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