1ITK

Crystal structure of catalase-peroxidase from Haloarcula marismortui

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.182 

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This is version 1.2 of the entry. See complete history. 


Literature

The 2.0 A crystal structure of catalase-peroxidase from Haloarcula marismortui.

Yamada, Y., Fujiwara, T., Sato, T., Igarashi, N., Tanaka, N.

(2002) Nat Struct Biol 9: 691-695

  • DOI: 10.1038/nsb834
  • Primary Citation of Related Structures:  
    1ITK

  • PubMed Abstract: 

    • Catalase-peroxidase is a member of the class I peroxidase superfamily. The enzyme exhibits both catalase and peroxidase activities to remove the harmful peroxide molecule from the living cell. The 2.0 A crystal structure of the catalase-peroxidase from Haloarcula marismortui (HmCP) reveals that the enzyme is a dimer of two identical subunits ...

    Catalase-peroxidase is a member of the class I peroxidase superfamily. The enzyme exhibits both catalase and peroxidase activities to remove the harmful peroxide molecule from the living cell. The 2.0 A crystal structure of the catalase-peroxidase from Haloarcula marismortui (HmCP) reveals that the enzyme is a dimer of two identical subunits. Each subunit is composed of two structurally homologous domains with a topology similar to that of class I peroxidase. The active site of HmCP is in the N-terminal domain. Although the arrangement of the catalytic residues and the cofactor heme b in the active site is virtually identical to that of class I peroxidases, the heme moiety is buried inside the domain, similar to that in a typical catalase. In the vicinity of the active site, novel covalent bonds are formed among the side chains of three residues, including that of a tryptophan on the distal side of the heme. Together with the C-terminal domain, these covalent bonds fix two long loops on the surface of the enzyme that cover the substrate access channel to the active site. These features provide an explanation for the dual activities of this enzyme.

    Organizational Affiliation: 

    Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
catalase-peroxidaseA, B731Haloarcula marismortuiMutation(s): 0 
EC: 1.11.1.6 (PDB Primary Data), 1.11.1.21 (UniProt)
UniProt
Find proteins for O59651 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore O59651 
Go to UniProtKB:  O59651
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59651
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
FA [auth B],
T [auth A]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
SO4
Query on SO4
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C [auth A],
D [auth A],
E [auth A],
F [auth A],
U [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
U [auth B],
V [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
CL
Query on CL
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G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
UNX
Query on UNX
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AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
S [auth A]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 317.632α = 90
b = 82.141β = 100.24
c = 75.102γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance