1x2b: Difference between revisions
New page: left|200px<br /><applet load="1x2b" size="450" color="white" frame="true" align="right" spinBox="true" caption="1x2b, resolution 2.40Å" /> '''The crystal structur... |
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[[Image:1x2b.gif|left|200px]]<br /><applet load="1x2b" size=" | [[Image:1x2b.gif|left|200px]]<br /><applet load="1x2b" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1x2b, resolution 2.40Å" /> | caption="1x2b, resolution 2.40Å" /> | ||
'''The crystal structure of prolyl aminopeptidase complexed with Sar-TBODA'''<br /> | '''The crystal structure of prolyl aminopeptidase complexed with Sar-TBODA'''<br /> | ||
==Overview== | ==Overview== | ||
The prolyl aminopeptidase complexes of Ala-TBODA | 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. | ||
==About this Structure== | ==About this Structure== | ||
1X2B is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens] with STX as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Prolyl_aminopeptidase Prolyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.5 3.4.11.5] Full crystallographic information is available from [http:// | 1X2B is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens] with <scene name='pdbligand=STX:'>STX</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Prolyl_aminopeptidase Prolyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.5 3.4.11.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X2B OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: prolyl iminopeptidase]] | [[Category: prolyl iminopeptidase]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:50:21 2008'' | ||
Revision as of 16:50, 21 February 2008
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The crystal structure of prolyl aminopeptidase complexed with Sar-TBODA
OverviewOverview
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.
About this StructureAbout this Structure
1X2B is a Single protein structure of sequence from Serratia marcescens with as ligand. Active as Prolyl aminopeptidase, with EC number 3.4.11.5 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
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