1x2b: Difference between revisions

Revision as of 23:12, 27 July 2008

This article has been automatically seeded. Changes to this page should pertain to the PDB entry only and not to the protein or biomolecule in general.

File:1x2b.png

Template:STRUCTURE 1x2b

The crystal structure of prolyl aminopeptidase complexed with Sar-TBODAThe crystal structure of prolyl aminopeptidase complexed with Sar-TBODA

Template:ABSTRACT PUBMED 16452443

About this StructureAbout this Structure

1X2B is a Single protein structure of sequence from Serratia marcescens. Full crystallographic information is available from OCA.

ReferenceReference

Unusual extra space at the active site and high activity for acetylated hydroxyproline of prolyl aminopeptidase from Serratia marcescens., Nakajima Y, Ito K, Sakata M, Xu Y, Nakashima K, Matsubara F, Hatakeyama S, Yoshimoto T, J Bacteriol. 2006 Feb;188(4):1599-606. PMID:16452443

Page seeded by OCA on Sun Jul 27 23:12:05 2008

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

OCA

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-[[Image:1x2b.gif|left|200px]]
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 {{STRUCTURE_1x2b|  PDB=1x2b  |  SCENE=  }}
-'''The crystal structure of prolyl aminopeptidase complexed with Sar-TBODA'''
+===The crystal structure of prolyl aminopeptidase complexed with Sar-TBODA===
-==Overview==
+<!--
-The prolyl aminopeptidase complexes of Ala-TBODA [2-alanyl-5-tert-butyl-(1, 3, 4)-oxadiazole] and Sar-TBODA [2-sarcosyl-5-tert-butyl-(1, 3, 4)-oxadiazole] were analyzed by X-ray crystallography at 2.4 angstroms resolution. Frames of alanine and sarcosine residues were well superimposed on each other in the pyrrolidine ring of proline residue, suggesting that Ala and Sar are recognized as parts of this ring of proline residue by the presence of a hydrophobic proline pocket at the active site. Interestingly, there was an unusual extra space at the bottom of the hydrophobic pocket where proline residue is fixed in the prolyl aminopeptidase. Moreover, 4-acetyloxyproline-betaNA (4-acetyloxyproline beta-naphthylamide) was a better substrate than Pro-betaNA. Computer docking simulation well supports the idea that the 4-acetyloxyl group of the substrate fitted into that space. Alanine scanning mutagenesis of Phe139, Tyr149, Tyr150, Phe236, and Cys271, consisting of the hydrophobic pocket, revealed that all of these five residues are involved significantly in the formation of the hydrophobic proline pocket for the substrate. Tyr149 and Cys271 may be important for the extra space and may orient the acetyl derivative of hydroxyproline to a preferable position for hydrolysis. These findings imply that the efficient degradation of collagen fragment may be achieved through an acetylation process by the bacteria.
+The line below this paragraph, {{ABSTRACT_PUBMED_16452443}}, adds the Publication Abstract to the page
+(as it appears on PubMed at http://www.pubmed.gov), where 16452443 is the PubMed ID number.
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+{{ABSTRACT_PUBMED_16452443}}
 ==About this Structure==
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 [[Category: Prolyl aminopeptidase]]
 [[Category: Prolyl iminopeptidase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 14:26:20 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 23:12:05 2008''