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PDBsum entry 1buq

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1buq
Jmol
Contents
Protein chains
125 a.a. *
Ligands
NTH ×2
* Residue conservation analysis
PDB id:
1buq
Name: Isomerase
Title: Solution structure of delta-5-3-ketosteroid isomerase complexed with the steroid 19-nortestosterone-hemisuccinate
Structure: Protein (3-ketosteroid isomerase-19- nortestosterone-hemisuccinate). Chain: a, b. Synonym: ksi. Engineered: yes. Mutation: yes. Other_details: ksi complexed with 19-nortestosterone- hemisuccinate, a substrate analog.
Source: Comamonas testosteroni. Organism_taxid: 285. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21/de3. Other_details: pet-25b+gene
NMR struc: 15 models
Authors: M.A.Massiah,C.Abeygunawardana,A.G.Gittis,A.S.Mildvan
Key ref:
M.A.Massiah et al. (1998). Solution structure of Delta 5-3-ketosteroid isomerase complexed with the steroid 19-nortestosterone hemisuccinate. Biochemistry, 37, 14701-14712. PubMed id: 9778345 DOI: 10.1021/bi981447b
Date:
04-Sep-98     Release date:   20-Jan-99    
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
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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
Bound ligand (Het Group name = NTH)
matches with 67.00% similarity
= 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: 10.1021/bi981447b Biochemistry 37:14701-14712 (1998)
PubMed id: 9778345  
 
 
Solution structure of Delta 5-3-ketosteroid isomerase complexed with the steroid 19-nortestosterone hemisuccinate.
M.A.Massiah, C.Abeygunawardana, A.G.Gittis, A.S.Mildvan.
 
  ABSTRACT  
 
The solution structure of the ketosteroid isomerase homodimer complexed with the product analogue 19-nortestosterone hemisuccinate (19-NTHS) was solved by heteronuclear multidimensional NMR methods using 1647 distance restraints, 77 dihedral angle (phi) restraints, and 67 hydrogen bond restraints per monomer. The refined secondary structure of each subunit consists of three alpha-helices, eight beta-strands, four turns, and two beta-bulges. The beta-strands form a mixed beta-sheet. One of the five proline residues, Pro-39, is cis and begins a nonclassical turn. A self-consistent ensemble of 15 tertiary/quaternary structures of the enzyme dimer-steroid complex, with no distance violations greater than 0.35 A, was generated by simulated annealing and energy minimization with the program X-PLOR. The mean pairwise RMSD of the secondary structural elements was 0.63 A for the average subunit and 1.25 A for the dimer. Within each subunit, the three alpha-helices are packed onto the concave surface of the beta-sheet with a groove between them into which the steroid binds at a site defined by 14 intermolecular distances. In the productive complex, Tyr-14, from alpha-helix 1, approaches both Asp-99 and the 3-keto group of 19-NTHS while, from beta-strand 1, the carboxylate of Asp-38 approaches the beta-face of the steroid near C4 and C6, between which it transfers a proton during catalysis. Thus the solution structure of the isomerase-steroid complex can accommodate the catalytic diad mechanism in which Asp-99 donates a hydrogen bond to Tyr-14 which in turn is hydrogen bonded to the 3-oxygen of the steroid. While direct hydrogen bonding of Asp-99 to the steroid oxygen is less likely, it cannot be excluded. All other interactions of the steroid with the enzyme are hydrophobic. The dimer interface, which is between the convex surfaces of the beta-sheets, is defined by 28 intersubunit NOEs between hydrophobic residues in the 13C-filtered NOESY-HSQC spectrum of a 13C/12C-heterolabeled dimer. Both hydrophobic and polar interactions occur at the dimer interface which contains no space that would permit additional steroid binding. Comparison of the complexed enzyme with the solution structure of the free enzyme [Wu et al. (1997) Science 276, 415-418] reveals that the three helices change position in the steroid complex, becoming more closely packed onto the concave surface of the beta-sheet, thus bringing Tyr-14 closer to Asp-99 and the substrate. Comparison of the enzyme-steroid complex in solution with the free enzyme in the crystalline state reveals similar differences between the positions of the helices.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
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.  
12770825 Y.Sun, X.Zhou, H.Dong, G.Tu, M.Wang, B.Wang, and Z.Deng (2003).
A complete gene cluster from Streptomyces nanchangensis NS3226 encoding biosynthesis of the polyether ionophore nanchangmycin.
  Chem Biol, 10, 431-441.  
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
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.  
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
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.  
10551849 H.S.Cho, N.C.Ha, G.Choi, H.J.Kim, D.Lee, K.S.Oh, K.S.Kim, W.Lee, K.Y.Choi, and B.H.Oh (1999).
Crystal structure of delta(5)-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin settles the correct hydrogen bonding scheme for transition state stabilization.
  J Biol Chem, 274, 32863-32868.
PDB code: 1qjg
10328262 T.K.Harris, and A.S.Mildvan (1999).
High-precision measurement of hydrogen bond lengths in proteins by nuclear magnetic resonance methods.
  Proteins, 35, 275-282.  
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.