1ogx
From Proteopedia
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==Overview== | ==Overview== | ||
| - | Delta(5)-3-Ketosteroid isomerase catalyzes cleavage and formation of a C-H | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1OGX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with <scene name='pdbligand=EQU:'>EQU</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure | + | 1OGX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with <scene name='pdbligand=EQU:'>EQU</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure supersedes the now removed PDB entry 1E3N. Active as [http://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] Known structural/functional Site: <scene name='pdbsite=AC1:Equ+Binding+Site+For+Chain+A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGX OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Steroid Delta-isomerase]] | [[Category: Steroid Delta-isomerase]] | ||
| - | [[Category: Ha, N | + | [[Category: Ha, N C.]] |
| - | [[Category: Kim, M | + | [[Category: Kim, M S.]] |
| - | [[Category: Oh, B | + | [[Category: Oh, B H.]] |
[[Category: EQU]] | [[Category: EQU]] | ||
[[Category: equilenin]] | [[Category: equilenin]] | ||
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[[Category: pi]] | [[Category: pi]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:17:43 2008'' |
Revision as of 12:17, 21 February 2008
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HIGH RESOLUTION CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE MUTANT D40N(D38N, TI NUMBERING) FROM PSEUDOMONAS PUTIDA COMPLEXED WITH EQUILENIN AT 2.0 A RESOLUTION.
Overview
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.
About this Structure
1OGX is a Single protein structure of sequence from Pseudomonas putida with as ligand. This structure supersedes the now removed PDB entry 1E3N. Active as Steroid Delta-isomerase, with EC number 5.3.3.1 Known structural/functional Site: . Full crystallographic information is available from OCA.
Reference
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., Ha NC, Kim MS, Lee W, Choi KY, Oh BH, J Biol Chem. 2000 Dec 29;275(52):41100-6. PMID:11007792
Page seeded by OCA on Thu Feb 21 14:17:43 2008
Categories: Pseudomonas putida | Single protein | Steroid Delta-isomerase | Ha, N C. | Kim, M S. | Oh, B H. | EQU | Equilenin | Isomerase | Ketosteroid isomerase | Ksi | Lbhb | Pi
