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PDBsum entry 3gyi

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protein ligands links
Oxidoreductase PDB id
3gyi
Jmol
Contents
Protein chain
498 a.a. *
Ligands
FAD
SO4
Waters ×683
* Residue conservation analysis
PDB id:
3gyi
Name: Oxidoreductase
Title: Cholesterol oxidase from streptomyces sp. N485d mutant (1.0a
Structure: Cholesterol oxidase. Chain: a. Synonym: chod. Engineered: yes. Mutation: yes
Source: Streptomyces sp.. Organism_taxid: 74576. Strain: sa-coo. Gene: choa. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.00Å     R-factor:   0.126     R-free:   0.158
Authors: A.Y.Lyubimov,A.Vrielink
Key ref:
A.Y.Lyubimov et al. (2009). A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase. Acta Crystallogr D Biol Crystallogr, 65, 1222-1231. PubMed id: 19923719 DOI: 10.1107/S0907444909037421
Date:
03-Apr-09     Release date:   01-Dec-09    
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 1 residue position (black cross)

 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 = FAD) 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: 10.1107/S0907444909037421 Acta Crystallogr D Biol Crystallogr 65:1222-1231 (2009)
PubMed id: 19923719  
 
 
A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase.
A.Y.Lyubimov, L.Chen, N.S.Sampson, A.Vrielink.
 
  ABSTRACT  
 
Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3beta-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH...pi interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall k(cat). Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 A resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH...pi interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Catalytic mechanism of cholesterol oxidase.
Figure 3.
Figure 3 Comparison of cholesterol oxidase active sites. (a) WT enzyme, (b) N485L mutant, (c) N485D mutant. Only the isoalloxazine portion of FAD is shown for clarity. Hydrogen bonds are shown as dashed lines. Water molecules are labeled W. Alternate conformations for side chains are labeled A and B.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2009, 65, 1222-1231) copyright 2009.  
  Figures were selected by an automated process.