1X2B

The crystal structure of prolyl aminopeptidase complexed with Sar-TBODA

Summary for 1X2B

• Entry DOI: 10.2210/pdb1x2b/pdb
• Related: 1QTR 1WM1 1X2E
• Descriptor: Proline iminopeptidase, 1-(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)-2-(METHYLAMINO)ETHANONE (3 entities in total)
• Functional Keywords: prolyl aminopeptidase, binary complex, prolyl iminopeptidase, alpha/beta-hydrolase, hydrolase
• Biological source: Serratia marcescens
• Cellular location: Cytoplasm: O32449
• Total number of polymer chains: 1
• Total formula weight: 36327.83

Authors

Nakajima, Y.,Ito, K.,Sakata, M.,Xu, Y.,Matsubara, F.,Hatakeyama, S.,Yoshimoto, T. (deposition date: 2005-04-22, release date: 2006-05-09, Last modification date: 2023-10-25)

Primary citation

Nakajima, Y.,Ito, K.,Sakata, M.,Xu, Y.,Nakashima, K.,Matsubara, F.,Hatakeyama, S.,Yoshimoto, T.
Unusual extra space at the active site and high activity for acetylated hydroxyproline of prolyl aminopeptidase from Serratia marcescens
J.Bacteriol., 188:1599-1606, 2006

PubMed Abstract: 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.

PubMed: 16452443
DOI: 10.1128/JB.188.4.1599-1606.2006

Experimental method

X-RAY DIFFRACTION (2.4 Å)