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PDBsum entry 1n1p

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protein ligands metals links
Oxidoreductase PDB id
1n1p
Jmol
Contents
Protein chain
499 a.a. *
Ligands
FAD
GOL
Metals
_MN ×3
Waters ×818
* Residue conservation analysis
PDB id:
1n1p
Name: Oxidoreductase
Title: Atomic resolution structure of cholesterol oxidase @ ph 7.4 (streptomyces sp. Sa-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: 1931. Gene: choa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
0.95Å     R-factor:   0.097     R-free:   0.119
Authors: A.Vrielink,P.I.Lario
Key ref: P.I.Lario and A.Vrielink (2003). Atomic resolution density maps reveal secondary structure dependent differences in electronic distribution. J Am Chem Soc, 125, 12787-12794. PubMed id: 14558826 DOI: 10.1021/ja0289954
Date:
18-Oct-02     Release date:   28-Oct-03    
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)
= 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/ja0289954 J Am Chem Soc 125:12787-12794 (2003)
PubMed id: 14558826  
 
 
Atomic resolution density maps reveal secondary structure dependent differences in electronic distribution.
P.I.Lario, A.Vrielink.
 
  ABSTRACT  
 
The X-ray crystal structure of the flavoenzyme cholesterol oxidase, SCOA (Streptomyces sp.SA-COO) has been determined to 0.95 A resolution. The large size (55kDa) and the high-resolution diffraction of this protein provides a unique opportunity to observe detailed electronic effects within a protein environment and to obtain a larger sampling for which to analyze these electronic and structural differences. It is well-known through spectroscopic methods that peptide carbonyl groups are polarized in alpha-helices. This electronic characteristic is evident in the sub-Angstrom electron density of SCOA. Our analysis indicates an increased tendency for the electron density of the main chain carbonyl groups within alpha-helices to be polarized toward the oxygen atoms. In contrast, the carbonyl groups in beta-sheet structures tend to exhibit a greater charge density between the carbon and oxygen atoms. Interestingly, the electronic differences observed at the carbonyl groups do not appear to be correlated to the bond distance of the peptide bond or the peptide planarity. This study gives important insight into the electronic effects of alpha-helix dipoles in enzymes and provides experimentally based observations that have not been previously characterized in protein structure.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20622857 G.J.Bartlett, A.Choudhary, R.T.Raines, and D.N.Woolfson (2010).
n-->pi* interactions in proteins.
  Nat Chem Biol, 6, 615-620.  
19469574 A.Choudhary, D.Gandla, G.R.Krow, and R.T.Raines (2009).
Nature of amide carbonyl--carbonyl interactions in proteins.
  J Am Chem Soc, 131, 7244-7246.  
18453693 B.Guillot, C.Jelsch, A.Podjarny, and C.Lecomte (2008).
Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.
  Acta Crystallogr D Biol Crystallogr, 64, 567-588.  
17020280 J.A.Hodges, and R.T.Raines (2006).
Energetics of an n --> pi interaction that impacts protein structure.
  Org Lett, 8, 4695-4697.  
16855309 T.C.Terwilliger, H.Klei, P.D.Adams, N.W.Moriarty, and J.D.Cohn (2006).
Automated ligand fitting by core-fragment fitting and extension into density.
  Acta Crystallogr D Biol Crystallogr, 62, 915-922.  
16121398 O.Koch, M.Bocola, and G.Klebe (2005).
Cooperative effects in hydrogen-bonding of protein secondary structure elements: a systematic analysis of crystal data using Secbase.
  Proteins, 61, 310-317.  
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.