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PDBsum entry 2cag

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Oxidoreductase (h2o2 acceptor) PDB id
2cag
Jmol
Contents
Protein chain
475 a.a. *
Ligands
HEM
Waters ×70
* Residue conservation analysis
PDB id:
2cag
Name: Oxidoreductase (h2o2 acceptor)
Title: Catalase compound ii
Structure: Catalase compound ii. Chain: a. Other_details: compound ii was obtained by reducing a cryst containing the protein in the compound i state with dithiot
Source: Proteus mirabilis. Organism_taxid: 584. Variant: peroxide resistant mutant. Organ: liver
Biol. unit: Tetramer (from PDB file)
Resolution:
2.70Å     R-factor:   0.179     R-free:   0.241
Authors: P.Gouet,H.M.Jouve,J.Hajdu
Key ref: P.Gouet et al. (1996). Ferryl intermediates of catalase captured by time-resolved Weissenberg crystallography and UV-VIS spectroscopy. Nat Struct Biol, 3, 951-956. PubMed id: 8901874
Date:
12-Jun-96     Release date:   07-Dec-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P42321  (CATA_PROMI) -  Catalase
Seq:
Struc:
484 a.a.
475 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.6  - Catalase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 H2O2 = O2 + 2 H2O
2 × H(2)O(2)
= O(2)
+ 2 × H(2)O
      Cofactor: Heme; Mn(2+)
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
Mn(2+)
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   3 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
Nat Struct Biol 3:951-956 (1996)
PubMed id: 8901874  
 
 
Ferryl intermediates of catalase captured by time-resolved Weissenberg crystallography and UV-VIS spectroscopy.
P.Gouet, H.M.Jouve, P.A.Williams, I.Andersson, P.Andreoletti, L.Nussaume, J.Hajdu.
 
  ABSTRACT  
 
Various enzymes use semi-stable ferryl intermediates and free radicals during their catalytic cycle, amongst them haem catalases. Structures for two transient intermediates (compounds I and II) of the NADPH-dependent catalase from Proteus mirabilis (PMC) have been determined by time-resolved X-ray crystallography and single crystal microspectrophotometry. The results show the formation and transformation of the ferryl group in the haem, and the unexpected binding of an anion during this reaction at a site distant from the haem.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21525643 A.M.Orville, R.Buono, M.Cowan, A.Héroux, G.Shea-McCarthy, D.K.Schneider, J.M.Skinner, M.J.Skinner, D.Stoner-Ma, and R.M.Sweet (2011).
Correlated single-crystal electronic absorption spectroscopy and X-ray crystallography at NSLS beamline X26-C.
  J Synchrotron Radiat, 18, 358-366.  
19240328 J.McGeehan, R.B.Ravelli, J.W.Murray, R.L.Owen, F.Cipriani, S.McSweeney, M.Weik, and E.F.Garman (2009).
Colouring cryo-cooled crystals: online microspectrophotometry.
  J Synchrotron Radiat, 16, 163-172.  
17565988 H.P.Hersleth, T.Uchida, A.K.Røhr, T.Teschner, V.Schünemann, T.Kitagawa, A.X.Trautwein, C.H.Görbitz, and K.K.Andersson (2007).
Crystallographic and spectroscopic studies of peroxide-derived myoglobin compound II and occurrence of protonated FeIV O.
  J Biol Chem, 282, 23372-23386.
PDB codes: 2v1e 2v1f 2v1g 2v1h 2v1i 2v1j 2v1k
17237942 O.Horner, J.M.Mouesca, P.L.Solari, M.Orio, J.L.Oddou, P.Bonville, and H.M.Jouve (2007).
Spectroscopic description of an unusual protonated ferryl species in the catalase from Proteus mirabilis and density functional theory calculations on related models. Consequences for the ferryl protonation state in catalase, peroxidase and chloroperoxidase.
  J Biol Inorg Chem, 12, 509-525.  
18021062 P.Nicholls (2007).
The oxygenase-peroxidase theory of Bach and Chodat and its modern equivalents: change and permanence in scientific thinking as shown by our understanding of the roles of water, peroxide, and oxygen in the functioning of redox enzymes.
  Biochemistry (Mosc), 72, 1039-1046.  
16895990 K.L.Stone, R.K.Behan, and M.T.Green (2006).
Resonance Raman spectroscopy of chloroperoxidase compound II provides direct evidence for the existence of an iron(IV)-hydroxide.
  Proc Natl Acad Sci U S A, 103, 12307-12310.  
15625113 M.L.Oldham, A.R.Brash, and M.E.Newcomer (2005).
The structure of coral allene oxide synthase reveals a catalase adapted for metabolism of a fatty acid hydroperoxide.
  Proc Natl Acad Sci U S A, 102, 297-302.
PDB code: 1u5u
15339813 K.Nilsson, H.P.Hersleth, T.H.Rod, K.K.Andersson, and U.Ryde (2004).
The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement.
  Biophys J, 87, 3437-3447.  
12486720 P.Andreoletti, G.Sainz, M.Jaquinod, J.Gagnon, and H.M.Jouve (2003).
High-resolution structure and biochemical properties of a recombinant Proteus mirabilis catalase depleted in iron.
  Proteins, 50, 261-271.
PDB codes: 1e93 1h6n
10698731 I.Schlichting, J.Berendzen, K.Chu, A.M.Stock, S.A.Maves, D.E.Benson, R.M.Sweet, D.Ringe, G.A.Petsko, and S.G.Sligar (2000).
The catalytic pathway of cytochrome p450cam at atomic resolution.
  Science, 287, 1615-1622.
PDB codes: 1dz4 1dz6 1dz8 1dz9
10318800 H.N.Kirkman, M.Rolfo, A.M.Ferraris, and G.F.Gaetani (1999).
Mechanisms of protection of catalase by NADPH. Kinetics and stoichiometry.
  J Biol Chem, 274, 13908-13914.  
9818266 B.L.Stoddard (1998).
New results using Laue diffraction and time-resolved crystallography.
  Curr Opin Struct Biol, 8, 612-618.  
  9144772 J.Bravo, I.Fita, J.C.Ferrer, W.Ens, A.Hillar, J.Switala, and P.C.Loewen (1997).
Identification of a novel bond between a histidine and the essential tyrosine in catalase HPII of Escherichia coli.
  Protein Sci, 6, 1016-1023.  
9345628 K.Moffat, and Z.Ren (1997).
Synchrotron radiation applications to macromolecular crystallography.
  Curr Opin Struct Biol, 7, 689-696.  
9407091 S.Bettati, L.D.Kwiatkowski, J.S.Kavanaugh, A.Mozzarelli, A.Arnone, G.L.Rossi, and R.W.Noble (1997).
Structure and oxygen affinity of crystalline des-his-146beta human hemoglobin in the T state.
  J Biol Chem, 272, 33077-33084.
PDB code: 1axf
8901863 B.L.Stoddard (1996).
Caught in a chemical trap.
  Nat Struct Biol, 3, 907-909.  
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.