PDBsum entry 1ggf

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
Jmol PyMol
Protein chains
727 a.a. *
PEO ×11
HEM ×2
Waters ×2025
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of catalase hpii from escherichia coli, variant his128asn, complex with hydrogen peroxide.
Structure: Catalase hpii. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
2.28Å     R-factor:   0.185     R-free:   0.254
Authors: W.R.Melik-Adamyan,J.Bravo,X.Carpena,J.Switala,M.J.Mate, I.Fita,P.C.Loewen
Key ref:
W.Melik-Adamyan et al. (2001). Substrate flow in catalases deduced from the crystal structures of active site variants of HPII from Escherichia coli. Proteins, 44, 270-281. PubMed id: 11455600 DOI: 10.1002/prot.1092
21-Aug-00     Release date:   30-Aug-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P21179  (CATE_ECOLI) -  Catalase HPII
753 a.a.
727 a.a.*
Key:    PfamA domain  PfamB 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)
Bound ligand (Het Group name = PEO)
corresponds exactly
= 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   2 terms 
  Biological process     oxidation-reduction process   6 terms 
  Biochemical function     oxidoreductase activity     7 terms  


DOI no: 10.1002/prot.1092 Proteins 44:270-281 (2001)
PubMed id: 11455600  
Substrate flow in catalases deduced from the crystal structures of active site variants of HPII from Escherichia coli.
W.Melik-Adamyan, J.Bravo, X.Carpena, J.Switala, M.J.Maté, I.Fita, P.C.Loewen.
The active site of heme catalases is buried deep inside a structurally highly conserved homotetramer. Channels leading to the active site have been identified as potential routes for substrate flow and product release, although evidence in support of this model is limited. To investigate further the role of protein structure and molecular channels in catalysis, the crystal structures of four active site variants of catalase HPII from Escherichia coli (His128Ala, His128Asn, Asn201Ala, and Asn201His) have been determined at approximately 2.0-A resolution. The solvent organization shows major rearrangements with respect to native HPII, not only in the vicinity of the replaced residues but also in the main molecular channel leading to the heme distal pocket. In the two inactive His128 variants, continuous chains of hydrogen bonded water molecules extend from the molecular surface to the heme distal pocket filling the main channel. The differences in continuity of solvent molecules between the native and variant structures illustrate how sensitive the solvent matrix is to subtle changes in structure. It is hypothesized that the slightly larger H(2)O(2) passing through the channel of the native enzyme will promote the formation of a continuous chain of solvent and peroxide. The structure of the His128Asn variant complexed with hydrogen peroxide has also been determined at 2.3-A resolution, revealing the existence of hydrogen peroxide binding sites both in the heme distal pocket and in the main channel. Unexpectedly, the largest changes in protein structure resulting from peroxide binding are clustered on the heme proximal side and mainly involve residues in only two subunits, leading to a departure from the 222-point group symmetry of the native enzyme. An active role for channels in the selective flow of substrates through the catalase molecule is proposed as an integral feature of the catalytic mechanism. The Asn201His variant of HPII was found to contain unoxidized heme b in combination with the proximal side His-Tyr bond suggesting that the mechanistic pathways of the two reactions can be uncoupled.
  Selected figure(s)  
Figure 1.
Figure 1. Stereo views of the heme environment. A: Native HPII. B: His128Ala variant. C: Asn201His variant. For clarity, only the catalytically important residues His128, Ser167, and Asn201 on the heme distal side and His392, Arg411, and Tyr415 on the heme proximal side are explicitly shown. Also displayed are the conserved residues lining the channel, Val169, Asp181, Phe207, and Phe217. The ring of hydrophobic residues that include Val169 define the narrowest point in the major channel. Heme d is evident only in native HPII (A), and the covalent bond between the side-chains of His392 and Tyr415 is evident in native HPII (A) and the Asn201His variant (C). Changes in solvent organization are evident among the three structures. Water molecules in the native enzyme, and their equivalent in the variants, are labeled numerically, W1-W8. Water molecules in the variant structures with no correspondence in native HPII are labeled alphabetically, WA-WE. [Color figure can be viewed in the online issue, which is available at].
Figure 2.
Figure 2. Stereo views showing the opening of the major channel into the heme distal side pocket in the His128Ala variant structure. A: Averaged omit (F[o] - F[c]) electron-density map shown with a chicken wire representation. Density corresponding to the chain of omitted water molecules is clearly defined filling the heme distal side pocket and the major channel. B: The accessible surface, calculated with the program VOIDOO, emphasizes the continuity of the channel and of the chain of solvent molecules found inside. Red spheres, water molecules; dashed lines, hydrogen bonds among water molecules in the channel; dotted lines, iron coordination.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2001, 44, 270-281) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18638417 L.Gabison, T.Prangé, N.Colloc'h, M.El Hajji, B.Castro, and M.Chiadmi (2008).
Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: mechanistic implications.
  BMC Struct Biol, 8, 32.
PDB codes: 3bjp 3bk8
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.  
16858726 J.P.Lasserre, E.Beyne, S.Pyndiah, D.Lapaillerie, S.Claverol, and M.Bonneu (2006).
A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis.
  Electrophoresis, 27, 3306-3321.  
15317589 H.Danielsson Thorell, N.H.Beyer, N.H.Heegaard, M.Ohman, and T.Nilsson (2004).
Comparison of native and recombinant chlorite dismutase from Ideonella dechloratans.
  Eur J Biochem, 271, 3539-3546.  
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
12777389 P.Chelikani, X.Carpena, I.Fita, and P.C.Loewen (2003).
An electrical potential in the access channel of catalases enhances catalysis.
  J Biol Chem, 278, 31290-31296.
PDB codes: 1p7y 1p7z 1p80 1p81 1qws
12454454 G.N.Murshudov, A.I.Grebenko, J.A.Brannigan, A.A.Antson, V.V.Barynin, G.G.Dodson, Z.Dauter, K.S.Wilson, and W.R.Melik-Adamyan (2002).
The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex.
  Acta Crystallogr D Biol Crystallogr, 58, 1972-1982.
PDB codes: 1gwe 1gwf 1gwh
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.