1E3V

Crystal structure of ketosteroid isomerase from Psedomonas putida complexed with deoxycholate

Summary for 1E3V

• Entry DOI: 10.2210/pdb1e3v/pdb
• Related: 1C7H 1DMN 1DMQ 1E3N 1E3R 1E97 1OPY 4TSU
• Descriptor: STEROID DELTA-ISOMERASE, (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID (3 entities in total)
• Functional Keywords: isomerase, deoxychlate, ksi, lbhb, reverse binding
• Biological source: PSEUDOMONAS PUTIDA
• Total number of polymer chains: 2
• Total formula weight: 29882.15

Authors

Ha, N.-C.,Kim, M.-S.,Kim, J.-S.,Oh, B.-H. (deposition date: 2000-06-24, release date: 2001-03-12, Last modification date: 2024-05-08)

Primary citation

Ha, N.-C.,Kim, M.-S.,Lee, W.,Choi, K.Y.,Oh, B.-H.
Detection of Large Pka Perturbations of an Inhibitor and a Catalytic Group at an Enzyme Active Site, a Mechanistic Basis for Catalytic Power of Many Enzymes
J.Biol.Chem., 275:41100-, 2000

PubMed Abstract: Delta(5)-3-Ketosteroid isomerase catalyzes cleavage and formation of a C-H bond at a diffusion-controlled limit. By determining the crystal structures of the enzyme in complex with each of three different inhibitors and by nuclear magnetic resonance (NMR) spectroscopic investigation, we evidenced the ionization of a hydroxyl group (pK(a) approximately 16.5) of an inhibitor, which forms a low barrier hydrogen bond (LBHB) with a catalytic residue Tyr(14) (pK(a) approximately 11.5), and the protonation of the catalytic residue Asp(38) with pK(a) of approximately 4.5 at pH 6.7 in the interaction with a carboxylate group of an inhibitor. The perturbation of the pK(a) values in both cases arises from the formation of favorable interactions between inhibitors and catalytic residues. The results indicate that the pK(a) difference between catalytic residue and substrate can be significantly reduced in the active site environment as a result of the formation of energetically favorable interactions during the course of enzyme reactions. The reduction in the pK(a) difference should facilitate the abstraction of a proton and thereby eliminate a large fraction of activation energy in general acid/base enzyme reactions. The pK(a) perturbation provides a mechanistic ground for the fast reactivity of many enzymes and for the understanding of how some enzymes are able to extract a proton from a C-H group with a pK(a) value as high as approximately 30.

PubMed: 11007792
DOI: 10.1074/JBC.M007561200

Experimental method

X-RAY DIFFRACTION (2 Å)