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PDBsum entry 1i19

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1i19
Jmol
Contents
Protein chains
541 a.a. *
Ligands
EDO ×12
FAD ×2
CAC
Metals
_MN ×3
Waters ×1009
* Residue conservation analysis
PDB id:
1i19
Name: Oxidoreductase
Title: Crystal structure of cholesterol oxidase from b.Sterolicum
Structure: Cholesterol oxidase. Chain: a, b. Engineered: yes. Other_details: covalent fad
Source: Brevibacterium sterolicum. Organism_taxid: 1702. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.70Å     R-factor:   0.182     R-free:   0.201
Authors: R.Coulombe,K.Q.Yue,S.Ghisla,A.Vrielink
Key ref:
R.Coulombe et al. (2001). Oxygen access to the active site of cholesterol oxidase through a narrow channel is gated by an Arg-Glu pair. J Biol Chem, 276, 30435-30441. PubMed id: 11397813 DOI: 10.1074/jbc.M104103200
Date:
31-Jan-01     Release date:   08-Aug-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q7SID9  (Q7SID9_BREST) -  Oxidoreductase
Seq:
Struc:
 
Seq:
Struc:
561 a.a.
541 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1074/jbc.M104103200 J Biol Chem 276:30435-30441 (2001)
PubMed id: 11397813  
 
 
Oxygen access to the active site of cholesterol oxidase through a narrow channel is gated by an Arg-Glu pair.
R.Coulombe, K.Q.Yue, S.Ghisla, A.Vrielink.
 
  ABSTRACT  
 
Cholesterol oxidase is a monomeric flavoenzyme that catalyzes the oxidation and isomerization of cholesterol to cholest-4-en-3-one. Two forms of the enzyme are known, one containing the cofactor non-covalently bound to the protein and one in which the cofactor is covalently linked to a histidine residue. The x-ray structure of the enzyme from Brevibacterium sterolicum containing covalently bound FAD has been determined and refined to 1.7-A resolution. The active site consists of a cavity sealed off from the exterior of the protein. A model for the steroid substrate, cholesterol, can be positioned in the pocket revealing the structural factors that result in different substrate binding affinities between the two known forms of the enzyme. The structure suggests that Glu(475), located at the active site cavity, may act as the base for both the oxidation and the isomerization steps of the catalytic reaction. A water-filled channel extending toward the flavin moiety, inside the substrate-binding cavity, may act as the entry point for molecular oxygen for the oxidative half-reaction. An arginine and a glutamate residue at the active site, found in two conformations are proposed to control oxygen access to the cavity from the channel. These concerted side chain movements provide an explanation for the biphasic mode of reaction with dioxygen and the ping-pong kinetic mechanism exhibited by the enzyme.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. a, topology diagram for cholesterol oxidase. The strands and helices are numbered in the order that they appear in the primary sequence. b, stereo figure showing a ribbon representation of BCO2 (produced with the program Molscript (31)). The FAD cofactor and His 121 are shown in a ball-and-stick representation with white colored bonds. c, stereo figure showing the carbon trace of BCO2 with various residues along the chain tracing labeled. The FAD-binding domain is colored blue and the substrate-binding domain is red. The FAD cofactor is shown as a yellow stick representation.
Figure 4.
Fig. 4. The figure contains a stereo view showing (a) the gate open conformation and (b) the gate closed conformation of the active site. The bound ethanediol molecule is labeled as EDO and water molecules are shown as red spheres. c, surface representation showing the proposed oxygen channel with the gate open, and d, the gate closed conformation at the active site. The molecular surface is constructed using the program GRASP (32). The protein main chain is shown as a green coil. The FAD cofactor is shown in yellow, the side chains for Arg477 and Glu475 are included and the water molecules are shown as red CPK spheres.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 30435-30441) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21425316 J.Sedzik, and J.P.Jastrzebski (2011).
High-resolution structural model of porcine P2 myelin membrane protein with associated fatty acid ligand: Fact or artifact?
  J Neurosci Res, 89, 909-920.  
21183988 Y.W.Tan, and H.Yang (2011).
Seeing the forest for the trees: fluorescence studies of single enzymes in the context of ensemble experiments.
  Phys Chem Chem Phys, 13, 1709-1721.  
20409334 F.Volontè, L.Pollegioni, G.Molla, L.Frattini, F.Marinelli, and L.Piubelli (2010).
Production of recombinant cholesterol oxidase containing covalently bound FAD in Escherichia coli.
  BMC Biotechnol, 10, 33.  
19926290 H.X.Zhou, and J.A.McCammon (2010).
The gates of ion channels and enzymes.
  Trends Biochem Sci, 35, 179-185.  
19438712 D.P.Heuts, N.S.Scrutton, W.S.McIntire, and M.W.Fraaije (2009).
What's in a covalent bond? On the role and formation of covalently bound flavin cofactors.
  FEBS J, 276, 3405-3427.  
19015844 N.Doukyu, K.Shibata, H.Ogino, and M.Sagermann (2009).
Cloning, sequence analysis, and expression of a gene encoding Chromobacterium sp. DS-1 cholesterol oxidase.
  Appl Microbiol Biotechnol, 82, 479-490.  
19495743 N.Doukyu (2009).
Characteristics and biotechnological applications of microbial cholesterol oxidases.
  Appl Microbiol Biotechnol, 83, 825-837.  
18633481 J.F.Aparicio, and J.F.Martín (2008).
Microbial cholesterol oxidases: bioconversion enzymes or signal proteins?
  Mol Biosyst, 4, 804-809.  
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
18029419 A.Y.Lyubimov, K.Heard, H.Tang, N.S.Sampson, and A.Vrielink (2007).
Distortion of flavin geometry is linked to ligand binding in cholesterol oxidase.
  Protein Sci, 16, 2647-2656.
PDB codes: 3b3r 3b6d
17675410 J.Saam, I.Ivanov, M.Walther, H.G.Holzhütter, and H.Kuhn (2007).
Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels.
  Proc Natl Acad Sci U S A, 104, 13319-13324.  
16600599 A.Mattevi (2006).
To be or not to be an oxidase: challenging the oxygen reactivity of flavoenzymes.
  Trends Biochem Sci, 31, 276-283.  
17046020 I.M.Moustafa, S.Foster, A.Y.Lyubimov, and A.Vrielink (2006).
Crystal structure of LAAO from Calloselasma rhodostoma with an L-phenylalanine substrate: insights into structure and mechanism.
  J Mol Biol, 364, 991.
PDB code: 2iid
16698554 J.H.Han, N.Kerrison, C.Chothia, and S.A.Teichmann (2006).
Divergence of interdomain geometry in two-domain proteins.
  Structure, 14, 935-945.  
14675549 A.Vrielink, and N.Sampson (2003).
Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?
  Curr Opin Struct Biol, 13, 709-715.  
14690428 M.Ghanem, F.Fan, K.Francis, and G.Gadda (2003).
Spectroscopic and kinetic properties of recombinant choline oxidase from Arthrobacter globiformis.
  Biochemistry, 42, 15179-15188.  
12454495 R.Aunpad, S.P.Muench, P.J.Baker, S.Sedelnikova, W.Panbangred, N.Doukyu, R.Aono, and D.W.Rice (2002).
Crystallization and preliminary X-ray crystallographic studies on the class II cholesterol oxidase from Burkholderia cepacia containing bound flavin.
  Acta Crystallogr D Biol Crystallogr, 58, 2182-2183.  
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.