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PDBsum entry 1isk

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Isomerase PDB id
1isk
Jmol
Contents
Protein chains
125 a.a. *
* Residue conservation analysis
PDB id:
1isk
Name: Isomerase
Title: 3-oxo-delta5-steroid isomerase, nmr, 20 structures
Structure: 3-oxo-delta5-steroid isomerase. Chain: a, b. Synonym: ksi, 3-ketosteroid isomerase. Engineered: yes
Source: Comamonas testosteroni. Organism_taxid: 285. Atcc: 11996. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: Z.R.Wu,S.Ebrahimian,M.E.Zawrotny,L.D.Thornburg,G.C.Perez- Alvarado,P.Brothers,R.M.Pollack,M.F.Summers
Key ref:
Z.R.Wu et al. (1997). Solution structure of 3-oxo-delta5-steroid isomerase. Science, 276, 415-418. PubMed id: 9103200 DOI: 10.1126/science.276.5311.415
Date:
12-Mar-97     Release date:   12-Nov-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00947  (SDIS_COMTE) -  Steroid Delta-isomerase
Seq:
Struc:
125 a.a.
125 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.3.3.1  - Steroid Delta-isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A 3-oxo-Delta5-steroid = a 3-oxo-Delta4-steroid
3-oxo-Delta(5)-steroid
= 3-oxo-Delta(4)-steroid
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     transport   3 terms 
  Biochemical function     isomerase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1126/science.276.5311.415 Science 276:415-418 (1997)
PubMed id: 9103200  
 
 
Solution structure of 3-oxo-delta5-steroid isomerase.
Z.R.Wu, S.Ebrahimian, M.E.Zawrotny, L.D.Thornburg, G.C.Perez-Alvarado, P.Brothers, R.M.Pollack, M.F.Summers.
 
  ABSTRACT  
 
The three-dimensional structure of the enzyme 3-oxo-delta5-steroid isomerase (E.C. 5.3.3.1), a 28-kilodalton symmetrical dimer, was solved by multidimensional heteronuclear magnetic resonance spectroscopy. The two independently folded monomers pack together by means of extensive hydrophobic and electrostatic interactions. Each monomer comprises three alpha helices and a six-strand mixed beta-pleated sheet arranged to form a deep hydrophobic cavity. Catalytically important residues Tyr14 (general acid) and Asp38 (general base) are located near the bottom of the cavity and positioned as expected from mechanistic hypotheses. An unexpected acid group (Asp99) is also located in the active site adjacent to Tyr14, and kinetic and binding studies of the Asp99 to Ala mutant demonstrate that Asp99 contributes to catalysis by stabilizing the intermediate.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. (A) Stereoview showing the best fit superposition of the backbone C atoms of 20 distance-geometry models of the KSI-dimer^ generated with DIANA (23). Higher convergence is observed when^ the superposition is performed for the monomeric subunits (B)^ resulting from a small amount of disorder at the dimer interface^ (Table 1). (C) Schematic diagram showing the secondary^ structure of the KSI sheet. The sheet contains a significant^ kink along the axis denoted by arrows.
Figure 3.
Fig. 3. Surface representation of KSI, colored according to electrostatic potential, showing the acidic nature of the active site^ cavity. A substrate molecule (5-androstene-3,17-dione) docked^ computationally in an orientation consistent with the postulated^ mechanism and experimental NMR data (25) is also shown in a^ ball-and-stick representation.
 
  The above figures are reprinted by permission from the AAAs: Science (1997, 276, 415-418) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20405079 H.M.Lee, A.Kumar, M.Kołaski, D.Y.Kim, E.C.Lee, S.K.Min, M.Park, Y.C.Choi, and K.S.Kim (2010).
Comparison of cationic, anionic and neutral hydrogen bonded dimers.
  Phys Chem Chem Phys, 12, 6278-6287.  
20664863 Y.Z.Chen, Y.H.Tian, M.Kertesz, and R.G.Weiss (2010).
Why is there no in-plane H-atom transfer from aryloxy radicals? A theoretical and experimental investigation.
  Photochem Photobiol Sci, 9, 1203-1211.  
19799395 D.K.Chakravorty, A.V.Soudackov, and S.Hammes-Schiffer (2009).
Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: analysis of hydrogen bonding, conformational motions, and electrostatics.
  Biochemistry, 48, 10608-10619.  
19706511 J.P.Schwans, D.A.Kraut, and D.Herschlag (2009).
Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase.
  Proc Natl Acad Sci U S A, 106, 14271-14275.  
18424811 H.J.Lee, Y.J.Yoon, d.o. .S.Jang, C.Kim, H.J.Cha, B.H.Hong, K.Y.Choi, and H.C.Lee (2008).
15N NMR relaxation studies of Y14F mutant of ketosteroid isomerase: the influence of mutation on backbone mobility.
  J Biochem, 144, 159-166.  
16602823 D.A.Kraut, P.A.Sigala, B.Pybus, C.W.Liu, D.Ringe, G.A.Petsko, and D.Herschlag (2006).
Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  PLoS Biol, 4, e99.
PDB codes: 2b32 2pzv
16477668 H.Cybulski, E.Tymińska, and J.Sadlej (2006).
The properties of weak and strong dihydrogen-bonded D-H...H-A complexes.
  Chemphyschem, 7, 629-639.  
16040747 M.J.Yonkunas, Y.Xu, and P.Tang (2005).
Anesthetic interaction with ketosteroid isomerase: insights from molecular dynamics simulations.
  Biophys J, 89, 2350-2356.  
15819878 S.Rajagopal, and S.Vishveshwara (2005).
Short hydrogen bonds in proteins.
  FEBS J, 272, 1819-1832.  
15819891 Y.S.Yun, G.H.Nam, Y.G.Kim, B.H.Oh, and K.Y.Choi (2005).
Small exterior hydrophobic cluster contributes to conformational stability and steroid binding in ketosteroid isomerase from Pseudomonas putida biotype B.
  FEBS J, 272, 1999-2011.
PDB code: 1w6y
12704087 D.A.Kraut, K.S.Carroll, and D.Herschlag (2003).
Challenges in enzyme mechanism and energetics.
  Annu Rev Biochem, 72, 517-571.  
12389036 D.Lim, and N.C.Strynadka (2002).
Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus.
  Nat Struct Biol, 9, 870-876.
PDB codes: 1mwr 1mws 1mwt 1mwu 1mwx 1vqq
11841202 Z.Shi, B.A.Krantz, N.Kallenbach, and T.R.Sosnick (2002).
Contribution of hydrogen bonding to protein stability estimated from isotope effects.
  Biochemistry, 41, 2120-2129.  
11274465 D.H.Kim, G.H.Nam, D.S.Jang, S.Yun, G.Choi, H.C.Lee, and K.Y.Choi (2001).
Roles of dimerization in folding and stability of ketosteroid isomerase from Pseudomonas putida biotype B.
  Protein Sci, 10, 741-752.  
11389596 G.Choi, N.C.Ha, M.S.Kim, B.H.Hong, B.H.Oh, and K.Y.Choi (2001).
Pseudoreversion of the catalytic activity of Y14F by the additional substitution(s) of tyrosine with phenylalanine in the hydrogen bond network of delta 5-3-ketosteroid isomerase from Pseudomonas putida biotype B.
  Biochemistry, 40, 6828-6835.
PDB codes: 1e97 1ea2
11746694 Y.Nagata, K.Mori, M.Takagi, A.G.Murzin, and J.Damborský (2001).
Identification of protein fold and catalytic residues of gamma-hexachlorocyclohexane dehydrochlorinase LinA.
  Proteins, 45, 471-477.  
10769113 D.H.Kim, D.S.Jang, G.H.Nam, G.Choi, J.S.Kim, N.C.Ha, M.S.Kim, B.H.Oh, and K.Y.Choi (2000).
Contribution of the hydrogen-bond network involving a tyrosine triad in the active site to the structure and function of a highly proficient ketosteroid isomerase from Pseudomonas putida biotype B.
  Biochemistry, 39, 4581-4589.
PDB codes: 1dmm 1dmn 1dmq
11041875 D.H.Kim, D.S.Jang, G.H.Nam, S.Yun, J.H.Cho, G.Choi, H.C.Lee, and K.Y.Choi (2000).
Equilibrium and kinetic analysis of folding of ketosteroid isomerase from Comamonas testosteroni.
  Biochemistry, 39, 13084-13092.  
10727228 F.Hénot, and R.M.Pollack (2000).
Catalytic activity of the D38A mutant of 3-oxo-Delta 5-steroid isomerase: recruitment of aspartate-99 as the base.
  Biochemistry, 39, 3351-3359.  
10653633 G.Choi, N.C.Ha, S.W.Kim, D.H.Kim, S.Park, B.H.Oh, and K.Y.Choi (2000).
Asp-99 donates a hydrogen bond not to Tyr-14 but to the steroid directly in the catalytic mechanism of Delta 5-3-ketosteroid isomerase from Pseudomonas putida biotype B.
  Biochemistry, 39, 903-909.
PDB code: 1cqs
10625485 I.P.Petrounia, G.Blotny, and R.M.Pollack (2000).
Binding of 2-naphthols to D38E mutants of 3-oxo-Delta 5-steroid isomerase: variation of ligand ionization state with the nature of the electrophilic component.
  Biochemistry, 39, 110-116.  
10841545 K.S.Kim, K.S.Oh, and J.Y.Lee (2000).
Catalytic role of enzymes: short strong H-bond-induced partial proton shuttles and charge redistributions.
  Proc Natl Acad Sci U S A, 97, 6373-6378.  
11076530 K.S.Oh, S.S.Cha, D.H.Kim, H.S.Cho, N.C.Ha, G.Choi, J.Y.Lee, P.Tarakeshwar, H.S.Son, K.Y.Choi, B.H.Oh, and K.S.Kim (2000).
Role of catalytic residues in enzymatic mechanisms of homologous ketosteroid isomerases.
  Biochemistry, 39, 13891-13896.  
11108473 Y.Xu, D.Xu, O.H.Crawford, and J.R.Einstein (2000).
A computational method for NMR-constrained protein threading.
  J Comput Biol, 7, 449-467.  
10360941 A.B.Taylor, W.H.Johnson, R.M.Czerwinski, H.S.Li, M.L.Hackert, and C.P.Whitman (1999).
Crystal structure of macrophage migration inhibitory factor complexed with (E)-2-fluoro-p-hydroxycinnamate at 1.8 A resolution: implications for enzymatic catalysis and inhibition.
  Biochemistry, 38, 7444-7452.
PDB code: 1mfi
9778344 A.B.Taylor, R.M.Czerwinski, W.H.Johnson, C.P.Whitman, and M.L.Hackert (1998).
Crystal structure of 4-oxalocrotonate tautomerase inactivated by 2-oxo-3-pentynoate at 2.4 A resolution: analysis and implications for the mechanism of inactivation and catalysis.
  Biochemistry, 37, 14692-14700.
PDB code: 1bjp
9666335 A.G.Murzin (1998).
How far divergent evolution goes in proteins.
  Curr Opin Struct Biol, 8, 380-387.  
9657686 B.Brooks, R.S.Phillips, and W.F.Benisek (1998).
High-efficiency incorporation in vivo of tyrosine analogues with altered hydroxyl acidity in place of the catalytic tyrosine-14 of Delta 5-3-ketosteroid isomerase of Comamonas (Pseudomonas) testosteroni: effects of the modifications on isomerase kinetics.
  Biochemistry, 37, 9738-9742.  
9622484 H.S.Cho, G.Choi, K.Y.Choi, and B.H.Oh (1998).
Crystal structure and enzyme mechanism of Delta 5-3-ketosteroid isomerase from Pseudomonas testosteroni.
  Biochemistry, 37, 8325-8330.
PDB code: 8cho
9622495 I.Rudik, S.Ghisla, and C.Thorpe (1998).
Protonic equilibria in the reductive half-reaction of the medium-chain acyl-CoA dehydrogenase.
  Biochemistry, 37, 8437-8445.  
9657682 J.M.Jez, and T.M.Penning (1998).
Engineering steroid 5 beta-reductase activity into rat liver 3 alpha-hydroxysteroid dehydrogenase.
  Biochemistry, 37, 9695-9703.  
9671521 L.D.Thornburg, F.Hénot, D.P.Bash, D.C.Hawkinson, S.D.Bartel, and R.M.Pollack (1998).
Electrophilic assistance by Asp-99 of 3-oxo-Delta 5-steroid isomerase.
  Biochemistry, 37, 10499-10506.  
9578560 L.Qi, and R.M.Pollack (1998).
Catalytic contribution of phenylalanine-101 of 3-oxo-Delta 5-steroid isomerase.
  Biochemistry, 37, 6760-6766.  
9778345 M.A.Massiah, C.Abeygunawardana, A.G.Gittis, and A.S.Mildvan (1998).
Solution structure of Delta 5-3-ketosteroid isomerase complexed with the steroid 19-nortestosterone hemisuccinate.
  Biochemistry, 37, 14701-14712.
PDB code: 1buq
9342312 C.H.Lin, T.Z.Hoffman, P.Wirsching, C.F.Barbas, K.D.Janda, and R.A.Lerner (1997).
On roads not taken in the evolution of protein catalysts: antibody steroid isomerases that use an enamine mechanism.
  Proc Natl Acad Sci U S A, 94, 11773-11776.  
  9401033 S.W.Kim, S.Joo, G.Choi, H.S.Cho, B.H.Oh, and K.Y.Choi (1997).
Mutational analysis of the three cysteines and active-site aspartic acid 103 of ketosteroid isomerase from Pseudomonas putida biotype B.
  J Bacteriol, 179, 7742-7747.  
9369474 S.W.Kim, S.S.Cha, H.S.Cho, J.S.Kim, N.C.Ha, M.J.Cho, S.Joo, K.K.Kim, K.Y.Choi, and B.H.Oh (1997).
High-resolution crystal structures of delta5-3-ketosteroid isomerase with and without a reaction intermediate analogue.
  Biochemistry, 36, 14030-14036.
PDB codes: 1oh0 1opy 4tsu
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.