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PDBsum entry 1yrc

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protein ligands metals links
Oxidoreductase PDB id
1yrc
Jmol
Contents
Protein chain
405 a.a. *
Ligands
HEM
CAM
Metals
__K
Waters ×489
* Residue conservation analysis
PDB id:
1yrc
Name: Oxidoreductase
Title: X-ray crystal structure of hydrogenated cytochrome p450cam
Structure: Cytochrome p450-cam. Chain: a. Synonym: camphor 5-monooxygenase, p450cam. Engineered: yes
Source: Pseudomonas putida. Organism_taxid: 303. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.40Å     R-factor:   0.202     R-free:   0.219
Authors: F.Meilleur,M.-T.Dauvergne,I.Schlichting,D.A.A.Myles
Key ref:
F.Meilleur et al. (2005). Production and X-ray crystallographic analysis of fully deuterated cytochrome P450cam. Acta Crystallogr D Biol Crystallogr, 61, 539-544. PubMed id: 15858263 DOI: 10.1107/S0907444905003872
Date:
03-Feb-05     Release date:   15-Feb-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00183  (CPXA_PSEPU) -  Camphor 5-monooxygenase
Seq:
Struc:
415 a.a.
405 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.15.1  - Camphor 5-monooxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: +-camphor + reduced putidaredoxin + O2 = +-exo-5-hydroxycamphor + oxidized putidaredoxin + H2O
(+)-camphor
Bound ligand (Het Group name = CAM)
corresponds exactly
+ reduced putidaredoxin
+ O(2)
= (+)-exo-5-hydroxycamphor
+ oxidized putidaredoxin
+ H(2)O
      Cofactor: Heme-thiolate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444905003872 Acta Crystallogr D Biol Crystallogr 61:539-544 (2005)
PubMed id: 15858263  
 
 
Production and X-ray crystallographic analysis of fully deuterated cytochrome P450cam.
F.Meilleur, M.T.Dauvergne, I.Schlichting, D.A.Myles.
 
  ABSTRACT  
 
Neutron protein crystallography allows H-atom positions to be located in biological structures at the relatively modest resolution of 1.5-2.0 A. A difficulty of this technique arises from the incoherent scattering from hydrogen, which considerably reduces the signal-to-noise ratio of the data. This can be overcome by preparing fully deuterated samples. Efficient protocols for routine and low-cost production of in vivo deuterium-enriched proteins have been developed. Here, the overexpression and crystallization of highly (>99%) deuterium-enriched cytochrome P450cam for neutron analysis is reported. Cytochrome P450cam from Pseudomonas putida catalyses the hydroxylation of camphor from haem-bound molecular O(2) via a mechanism that is thought to involve a proton-shuttle pathway to the active site. Since H atoms cannot be visualized in available X-ray structures, neutron diffraction is being used to determine the protonation states and water structure at the active site of the enzyme. Analysis of both hydrogenated and perdeuterated P450cam showed no significant changes between the X-ray structures determined at 1.4 and 1.7 A, respectively. This work demonstrates that the fully deuterated protein is highly isomorphous with the native (hydrogenated) protein and is appropriate for neutron protein crystallographic analysis.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Superposition of the active site showing the hydrogen bound between Tyr96 and the camphor carbonyl O atom, the Asp251 and Thr252 key residues and the internal water channel (W523, W566 and W687). Light blue, hydrogenated P450cam; blue, perdeuterated P450cam.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 539-544) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21171581 Y.T.Lee, E.C.Glazer, R.F.Wilson, C.D.Stout, and D.B.Goodin (2011).
Three clusters of conformational States in p450cam reveal a multistep pathway for closing of the substrate access channel .
  Biochemistry, 50, 693-703.  
20445231 A.S.Gardberg, A.R.Del Castillo, K.L.Weiss, F.Meilleur, M.P.Blakeley, and D.A.Myles (2010).
Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.
  Acta Crystallogr D Biol Crystallogr, 66, 558-567.
PDB codes: 3kyu 3kyv 3kyw 3kyx 3kyy
  20383004 M.M.Blum, S.J.Tomanicek, H.John, B.L.Hanson, H.Rüterjans, B.P.Schoenborn, P.Langan, and J.C.Chen (2010).
X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): perdeuteration of proteins for neutron diffraction.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 379-385.
PDB code: 3kgg
  19193991 K.Sakurai, H.Shimada, T.Hayashi, and T.Tsukihara (2009).
Substrate binding induces structural changes in cytochrome P450cam.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 80-83.
PDB codes: 2zwt 2zwu
16724195 E.H.Snell, M.J.van der Woerd, M.Damon, R.A.Judge, D.A.Myles, and F.Meilleur (2006).
Optimizing crystal volume for neutron diffraction: D-xylose isomerase.
  Eur Biophys J, 35, 621-632.  
16897039 F.Meilleur, D.A.Myles, and M.P.Blakeley (2006).
Neutron Laue macromolecular crystallography.
  Eur Biophys J, 35, 611-620.  
  16511248 M.Budayova-Spano, S.Z.Fisher, M.T.Dauvergne, M.Agbandje-McKenna, D.N.Silverman, D.A.Myles, and R.McKenna (2006).
Production and X-ray crystallographic analysis of fully deuterated human carbonic anhydrase II.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 6-9.
PDB code: 2ax2
16622654 M.P.Blakeley, A.Mitschler, I.Hazemann, F.Meilleur, D.A.Myles, and A.Podjarny (2006).
Comparison of hydrogen determination with X-ray and neutron crystallography in a human aldose reductase-inhibitor complex.
  Eur Biophys J, 35, 577-583.  
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.