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PDBsum entry 3b6d

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Oxidoreductase PDB id
3b6d
Jmol
Contents
Protein chain
498 a.a. *
Ligands
SO4
FAE
Waters ×560
* Residue conservation analysis
PDB id:
3b6d
Name: Oxidoreductase
Title: Crystal structure of streptomyces cholesterol oxidase h447q/ mutant (1.2a)
Structure: Cholesterol oxidase. Chain: a. Synonym: chod. Engineered: yes. Mutation: yes. Other_details: fad cofactor non-covalently bound to the enz
Source: Streptomyces sp.. Organism_taxid: 74576. Strain: sa-coo. Gene: choa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.20Å     R-factor:   0.133     R-free:   0.172
Authors: A.Y.Lyubimov,A.Vrielink
Key ref:
A.Y.Lyubimov et al. (2007). Distortion of flavin geometry is linked to ligand binding in cholesterol oxidase. Protein Sci, 16, 2647-2656. PubMed id: 18029419 DOI: 10.1110/ps.073168207
Date:
29-Oct-07     Release date:   18-Dec-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P12676  (CHOD_STRS0) -  Cholesterol oxidase
Seq:
Struc:
 
Seq:
Struc:
546 a.a.
498 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: E.C.1.1.3.6  - Cholesterol oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cholesterol + O2 = cholest-5-en-3-one + H2O2
Cholesterol
+ O(2)
= cholest-5-en-3-one
+ H(2)O(2)
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAE) corresponds exactly
   Enzyme class 3: 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
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1110/ps.073168207 Protein Sci 16:2647-2656 (2007)
PubMed id: 18029419  
 
 
Distortion of flavin geometry is linked to ligand binding in cholesterol oxidase.
A.Y.Lyubimov, K.Heard, H.Tang, N.S.Sampson, A.Vrielink.
 
  ABSTRACT  
 
Two high-resolution structures of a double mutant of bacterial cholesterol oxidase in the presence or absence of a ligand, glycerol, are presented, showing the trajectory of glycerol as it binds in a Michaelis complex-like position in the active site. A group of three aromatic residues forces the oxidized isoalloxazine moiety to bend along the N5-N10 axis as a response to the binding of glycerol in the active site. Movement of these aromatic residues is only observed in the glycerol-bound structure, indicating that some tuning of the FAD redox potential is caused by the formation of the Michaelis complex during regular catalysis. This structural study suggests a possible mechanism of substrate-assisted flavin activation, improves our understanding of the interplay between the enzyme, its flavin cofactor and its substrate, and is of use to the future design of effective cholesterol oxidase inhibitors.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Glycerol populations in the cholesterol oxidase active site. Ball-
 
  The above figure is reprinted by permission from the Protein Society: Protein Sci (2007, 16, 2647-2656) copyright 2007.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19923715 I.S.Fernández, F.J.Ruíz-Dueñas, E.Santillana, P.Ferreira, M.J.Martínez, A.T.Martínez, and A.Romero (2009).
Novel structural features in the GMC family of oxidoreductases revealed by the crystal structure of fungal aryl-alcohol oxidase.
  Acta Crystallogr D Biol Crystallogr, 65, 1196-1205.
PDB code: 3fim
18808119 P.A.Sigala, D.A.Kraut, J.M.Caaveiro, B.Pybus, E.A.Ruben, D.Ringe, G.A.Petsko, and D.Herschlag (2008).
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  J Am Chem Soc, 130, 13696-13708.
PDB codes: 2inx 3cpo
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 code is shown on the right.