spacer
spacer

PDBsum entry 1cc2

Go to PDB code: 
protein ligands links
Oxidoreductase PDB id
1cc2
Jmol
Contents
Protein chain
498 a.a. *
Ligands
FAD
Waters ×507
* Residue conservation analysis
PDB id:
1cc2
Name: Oxidoreductase
Title: Cholesterol oxidase from streptomyces his447gln mutant
Structure: Protein (cholesterol oxidase). Chain: a. Engineered: yes. Mutation: yes. Other_details: fad cofactor non-covalently bound to the enzyme
Source: Streptomyces sp.. Organism_taxid: 1931. Strain: bl21(de3). Variant: plyss. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: plyss.
Resolution:
2.20Å     R-factor:   0.147     R-free:   0.235
Authors: A.Vrielink,Q.K.Yue
Key ref:
Q.K.Yue et al. (1999). Crystal structure determination of cholesterol oxidase from Streptomyces and structural characterization of key active site mutants. Biochemistry, 38, 4277-4286. PubMed id: 10194345 DOI: 10.1021/bi982497j
Date:
03-Mar-99     Release date:   11-Mar-99    
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: 10.1021/bi982497j Biochemistry 38:4277-4286 (1999)
PubMed id: 10194345  
 
 
Crystal structure determination of cholesterol oxidase from Streptomyces and structural characterization of key active site mutants.
Q.K.Yue, I.J.Kass, N.S.Sampson, A.Vrielink.
 
  ABSTRACT  
 
Cholesterol oxidase is a monomeric flavoenzyme which catalyzes the oxidation and isomerization of cholesterol to cholest-4-en-3-one. The enzyme interacts with lipid bilayers in order to bind its steroid substrate. The X-ray structure of the enzyme from Brevibacterium sterolicum revealed two loops, comprising residues 78-87 and residues 433-436, which act as a lid over the active site and facilitate binding of the substrate [Vrielink et al. (1991) J. Mol. Biol. 219, 533-554; Li et al. (1993) Biochemistry 32, 11507-11515]. It was postulated that these loops must open, forming a hydrophobic channel between the membrane and the active site of the protein and thus sequestering the cholesterol substrate from the aqueous environment. Here we describe the three-dimensional structure of the homologous enzyme from Streptomyces refined to 1.5 A resolution. Structural comparisons to the enzyme from B. sterolicum reveal significant conformational differences in these loop regions; in particular, a region of the loop comprising residues 78-87 adopts a small amphipathic helical turn with hydrophobic residues directed toward the active site cavity and hydrophilic residues directed toward the external surface of the molecule. It seems reasonable that this increased rigidity reduces the entropy loss that occurs upon binding substrate. Consequently, the Streptomyces enzyme is a more efficient catalyst. In addition, we have determined the structures of three active site mutants which have significantly reduced activity for either the oxidation (His447Asn and His447Gln) or the isomerization (Glu361Gln). Our structural and kinetic data indicate that His447 and Glu361 act as general base catalysts in association with conserved water H2O541 and Asn485. The His447, Glu361, H2O541, and Asn485 hydrogen bond network is conserved among other oxidoreductases. This catalytic tetrad appears to be a structural motif that occurs in flavoenzymes that catalyze the oxidation of unactivated alcohols.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21208358 I.Uhía, B.Galán, V.Morales, and J.L.García (2011).
Initial step in the catabolism of cholesterol by Mycobacterium smegmatis mc2 155.
  Environ Microbiol, 13, 943-959.  
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.  
19923719 A.Y.Lyubimov, L.Chen, N.S.Sampson, and A.Vrielink (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.
PDB codes: 3gyi 3gyj
19843168 J.Kreit, and N.S.Sampson (2009).
Cholesterol oxidase: physiological functions.
  FEBS J, 276, 6844-6856.  
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.  
18296637 J.I.Yeh, U.Chinte, and S.Du (2008).
Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.
  Proc Natl Acad Sci U S A, 105, 3280-3285.
PDB codes: 2qcu 2r45 2r46 2r4e 2r4j
18063356 S.K.Arya, M.Datta, and B.D.Malhotra (2008).
Recent advances in cholesterol biosensor.
  Biosens Bioelectron, 23, 1083-1100.  
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
17668316 G.Gimpl, and K.Gehrig-Burger (2007).
Cholesterol reporter molecules.
  Biosci Rep, 27, 335-358.  
17379143 M.V.Mendes, E.Recio, N.Antón, S.M.Guerra, J.Santos-Aberturas, J.F.Martín, and J.F.Aparicio (2007).
Cholesterol oxidases act as signaling proteins for the biosynthesis of the polyene macrolide pimaricin.
  Chem Biol, 14, 279-290.  
17379137 N.M.Nesbitt, and N.S.Sampson (2007).
Antifungal tradecraft by cholesterol oxidase.
  Chem Biol, 14, 238-241.  
16604066 A.Y.Lyubimov, P.I.Lario, I.Moustafa, and A.Vrielink (2006).
Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment.
  Nat Chem Biol, 2, 259-264.
PDB codes: 1n4u 1n4v 1n4w 2gew
16999821 P.Ferreira, F.J.Ruiz-Dueñas, M.J.Martínez, W.J.van Berkel, and A.T.Martínez (2006).
Site-directed mutagenesis of selected residues at the active site of aryl-alcohol oxidase, an H2O2-producing ligninolytic enzyme.
  FEBS J, 273, 4878-4888.  
15661076 G.K.Kouassi, J.Irudayaraj, and G.McCarty (2005).
Examination of Cholesterol oxidase attachment to magnetic nanoparticles.
  J Nanobiotechnology, 3, 1.  
15817448 L.Caldinelli, S.Iametti, A.Barbiroli, F.Bonomi, D.Fessas, G.Molla, M.S.Pilone, and L.Pollegioni (2005).
Dissecting the structural determinants of the stability of cholesterol oxidase containing covalently bound flavin.
  J Biol Chem, 280, 22572-22581.  
15819617 R.D.Hayward, R.J.Cain, E.J.McGhie, N.Phillips, M.J.Garner, and V.Koronakis (2005).
Cholesterol binding by the bacterial type III translocon is essential for virulence effector delivery into mammalian cells.
  Mol Microbiol, 56, 590-603.  
15819891 Y.S.Yun, G.H.Nam, Y.G.Kim, B.H.Oh, and K.Y.Choi (2005).
Small exterior hydrophobic cluster contributes to conformational stability and steroid binding in ketosteroid isomerase from Pseudomonas putida biotype B.
  FEBS J, 272, 1999-2011.
PDB code: 1w6y
14675549 A.Vrielink, and N.Sampson (2003).
Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?
  Curr Opin Struct Biol, 13, 709-715.  
12591954 N.Friedland, H.L.Liou, P.Lobel, and A.M.Stock (2003).
Structure of a cholesterol-binding protein deficient in Niemann-Pick type C2 disease.
  Proc Natl Acad Sci U S A, 100, 2512-2517.
PDB code: 1nep
12192068 C.A.Bottoms, P.E.Smith, and J.J.Tanner (2002).
A structurally conserved water molecule in Rossmann dinucleotide-binding domains.
  Protein Sci, 11, 2125-2137.  
11790839 I.Dreveny, C.Kratky, and K.Gruber (2002).
The active site of hydroxynitrile lyase from Prunus amygdalus: modeling studies provide new insights into the mechanism of cyanogenesis.
  Protein Sci, 11, 292-300.  
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.  
11761331 N.S.Sampson (2001).
Dissection of a flavoenzyme active site: the reaction catalyzed by cholesterol oxidase.
  Antioxid Redox Signal, 3, 839-846.  
11514662 O.Dym, and D.Eisenberg (2001).
Sequence-structure analysis of FAD-containing proteins.
  Protein Sci, 10, 1712-1728.  
11063575 X.Chen, D.E.Wolfgang, and N.S.Sampson (2000).
Use of the parallax-quench method to determine the position of the active-site loop of cholesterol oxidase in lipid bilayers.
  Biochemistry, 39, 13383-13389.  
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.