PDBsum entry 1gwh

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Oxidoreductase PDB id
Protein chain
498 a.a. *
ACT ×2
Waters ×568
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Atomic resolution structure of micrococcus lysodeikticus catalase complexed with NADPH
Structure: Catalase. Chain: a. Ec:
Source: Micrococcus luteus. Organism_taxid: 1270
Biol. unit: Tetramer (from PDB file)
1.74Å     R-factor:   0.111     R-free:   0.138
Authors: G.N.Murshudov,A.I.Grebenko,J.A.Brannigan,A.A.Antson, V.V.Barynin,G.G.Dodson,Z.Dauter,K.S.Wilson, W.R.Melik-Adamyan
Key ref:
G.N.Murshudov et al. (2002). The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex. Acta Crystallogr D Biol Crystallogr, 58, 1972-1982. PubMed id: 12454454 DOI: 10.1107/S0907444902016566
15-Mar-02     Release date:   19-Mar-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P29422  (CATA_MICLU) -  Catalase
503 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: E.C.  - 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+)
Bound ligand (Het Group name = HEM) matches with 95.00% similarity
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  


DOI no: 10.1107/S0907444902016566 Acta Crystallogr D Biol Crystallogr 58:1972-1982 (2002)
PubMed id: 12454454  
The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex.
G.N.Murshudov, A.I.Grebenko, J.A.Brannigan, A.A.Antson, V.V.Barynin, G.G.Dodson, Z.Dauter, K.S.Wilson, W.R.Melik-Adamyan.
The crystal structure of the bacterial catalase from Micrococcus lysodeikticus has been refined using the gene-derived sequence both at 0.88 A resolution using data recorded at 110 K and at 1.5 A resolution with room-temperature data. The atomic resolution structure has been refined with individual anisotropic atomic thermal parameters. This has revealed the geometry of the haem and surrounding protein, including many of the H atoms, with unprecedented accuracy and has characterized functionally important hydrogen-bond interactions in the active site. The positions of the H atoms are consistent with the enzymatic mechanism previously suggested for beef liver catalase. The structure reveals that a 25 A long channel leading to the haem is filled by partially occupied water molecules, suggesting an inherent facile access to the active site. In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 A resolution and the catalase complex with NADPH at 1.83 A resolution have been determined. Comparison of compound II and the resting state of the enzyme shows that the binding of the O atom to the iron (bond length 1.87 A) is associated with increased haem bending and is accompanied by a distal movement of the iron and the side chain of the proximal tyrosine. Finally, the structure of the NADPH complex shows that the cofactor is bound to the molecule in an equivalent position to that found in beef liver catalase, but that only the adenine part of NADPH is visible in the present structure.
  Selected figure(s)  
Figure 1.
Figure 1 Stereoview of (a) ribbon diagram of the MLC tetramer and (b) CA trace of the M. lysodeikticus catalase monomer (in red) superimposed with that of beef liver catalase (in black). Figures were generated using MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]).
Figure 6.
Figure 6 (a) Electron density demonstrating oxygen binding to the haem Fe atom (orange) in compound II. C atoms are coloured grey, O atoms red and N atoms blue. The final 2F[o] - F[c] map (contoured at 1 level) is in blue. (b) Comparison of the active site in resting MLC-0.88 (red) with MLC-PAA (blue).
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1972-1982) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19652348 B.R.Goblirsch, B.R.Streit, J.L.DuBois, and C.M.Wilmot (2009).
Crystallization and preliminary X-ray diffraction of chlorite dismutase from Dechloromonas aromatica RCB.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 818-821.  
18586714 I.Georgiev, D.Keedy, J.S.Richardson, D.C.Richardson, and B.R.Donald (2008).
Algorithm for backrub motions in protein design.
  Bioinformatics, 24, i196-i204.  
17965160 M.A.Patrauchan, C.Florizone, S.Eapen, L.Gómez-Gil, B.Sethuraman, M.Fukuda, J.Davies, W.W.Mohn, and L.D.Eltis (2008).
Roles of ring-hydroxylating dioxygenases in styrene and benzene catabolism in Rhodococcus jostii RHA1.
  J Bacteriol, 190, 37-47.  
18174331 M.Newcomb, J.A.Halgrimson, J.H.Horner, E.C.Wasinger, L.X.Chen, and S.G.Sligar (2008).
X-ray absorption spectroscopic characterization of a cytochrome P450 compound II derivative.
  Proc Natl Acad Sci U S A, 105, 8179-8184.  
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.  
16609813 M.S.Lorentzen, E.Moe, H.M.Jouve, and N.P.Willassen (2006).
Cold adapted features of Vibrio salmonicida catalase: characterisation and comparison to the mesophilic counterpart from Proteus mirabilis.
  Extremophiles, 10, 427-440.  
16110518 C.Rovira (2005).
Structure, protonation state and dynamics of catalase compound II.
  Chemphyschem, 6, 1820-1826.  
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.