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PDBsum entry 1n4u

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Oxidoreductase PDB id
1n4u
Jmol
Contents
Protein chain
499 a.a. *
Ligands
PO4 ×5
FAE
OXY
GOL
Waters ×699
* Residue conservation analysis
PDB id:
1n4u
Name: Oxidoreductase
Title: Cholesterol oxidase from streptomyces @ ph 4.5 (streptomyces coo)
Structure: Cholesterol oxidase. Chain: a. Synonym: chod. Engineered: 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.
Biol. unit: Monomer (from PQS)
Resolution:
0.95Å     R-factor:   0.114     R-free:   0.136
Authors: A.Vrielink,P.I.Lario
Key ref:
A.Y.Lyubimov et al. (2006). Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment. Nat Chem Biol, 2, 259-264. PubMed id: 16604066 DOI: 10.1038/nchembio784
Date:
01-Nov-02     Release date:   27-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P12676  (CHOD_STRS0) -  Cholesterol oxidase
Seq:
Struc:
 
Seq:
Struc:
546 a.a.
499 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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)
Bound ligand (Het Group name = OXY)
corresponds exactly
= 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: 10.1038/nchembio784 Nat Chem Biol 2:259-264 (2006)
PubMed id: 16604066  
 
 
Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment.
A.Y.Lyubimov, P.I.Lario, I.Moustafa, A.Vrielink.
 
  ABSTRACT  
 
Hydrogen atoms are a vital component of enzyme structure and function. In recent years, atomic resolution crystallography (>or=1.2 A) has been successfully used to investigate the role of the hydrogen atom in enzymatic catalysis. Here, atomic resolution crystallography was used to study the effect of pH on cholesterol oxidase from Streptomyces sp., a flavoenzyme oxidoreductase. Crystallographic observations of the anionic oxidized flavin cofactor at basic pH are consistent with the UV-visible absorption profile of the enzyme and readily explain the reversible pH-dependent loss of oxidation activity. Furthermore, a hydrogen atom, positioned at an unusually short distance from the main chain carbonyl oxygen of Met122 at high pH, was observed, suggesting a previously unknown mechanism of cofactor stabilization. This study shows how a redox active site responds to changes in the enzyme's environment and how these changes are able to influence the mechanism of enzymatic catalysis.
 
  Selected figure(s)  
 
Figure 4.
(a–e) Electron-density features around the imidazole ring of His447 at pH 4.5 (a), pH 5.2 (b), pH 5.8 (c), pH 7.3 (d) and pH 9.0 (e). (f) A view of the interactions between His447, Asn321 and Asn323 at pH 5.2. The 2F[o] – F[c] density (magenta) is contoured at 4.0 , and the sharpened F[o] – F[c] density (green) is contoured at 2.0 . The atoms are depicted by a ball-and-stick representation. The bifurcated hydrogen bonds formed by ND1 of His447 with the amide groups of Asn321 and Asn323 are drawn as blue dashed lines. The chemical structure of the histidine side chain with labeled atoms is included.
Figure 5.
(a) A model representing the microenvironment from pH 4.5 to 7.3, where FAD is in the neutral oxidized form and His447 is in the imidazole form protonated at NE2. (b) A model representing the microenvironment at pH 9.0, where the negative charge of the imidazolate form of His447 is stabilized by interaction with Asn321 and Asn323.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2006, 2, 259-264) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21420915 Y.Xin, H.Yang, X.Xia, L.Zhang, C.Cheng, G.Mou, J.Shi, Y.Han, and W.Wang (2011).
Affinity purification of a cholesterol oxidase expressed in Escherichia coli.
  J Chromatogr B Analyt Technol Biomed Life Sci, 879, 853-858.  
19574215 P.Ferreira, A.Hernandez-Ortega, B.Herguedas, A.T.Martínez, and M.Medina (2009).
Aryl-alcohol oxidase involved in lignin degradation: a mechanistic study based on steady and pre-steady state kinetics and primary and solvent isotope effects with two alcohol substrates.
  J Biol Chem, 284, 24840-24847.  
19436071 S.R.Thomas, P.M.McTamney, J.M.Adler, N.Laronde-Leblanc, and S.E.Rokita (2009).
Crystal structure of iodotyrosine deiodinase, a novel flavoprotein responsible for iodide salvage in thyroid glands.
  J Biol Chem, 284, 19659-19667.
PDB codes: 3gb5 3gfd 3gh8
18410129 L.Chen, A.Y.Lyubimov, L.Brammer, A.Vrielink, and N.S.Sampson (2008).
The binding and release of oxygen and hydrogen peroxide are directed by a hydrophobic tunnel in cholesterol oxidase.
  Biochemistry, 47, 5368-5377.
PDB code: 3cnj
17085503 P.Shemella, B.Pereira, Y.Zhang, P.Van Roey, G.Belfort, S.Garde, and S.K.Nayak (2007).
Mechanism for intein C-terminal cleavage: a proposal from quantum mechanical calculations.
  Biophys J, 92, 847-853.  
17070680 L.De Colibus, and A.Mattevi (2006).
New frontiers in structural flavoenzymology.
  Curr Opin Struct Biol, 16, 722-728.  
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.