Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 57.87 kDa 
• Atom Count: 5144 
• Modelled Residue Count: 498 
• Deposited Residue Count: 503 
• Unique protein chains: 1

1GWE

Atomic resolution structure of Micrococcus Lysodeikticus catalase

• PDB DOI: 10.2210/pdb1GWE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Micrococcus luteus
• Mutation(s): No 


• Deposited: 2002-03-15 Released: 2002-04-26 
• Deposition Author(s): Murshudov, G.N., Grebenko, A.I., Brannigan, J.A., Antson, A.A., Barynin, V.V., Dodson, G.G., Dauter, Z., Wilson, K.S., Melik-Adamyan, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.88 Å
• R-Value Free: 0.096 
• R-Value Work: 0.089 
• R-Value Observed: 0.089 

Literature

The Structures of Micrococcus Lysodeikticus Catalase, its Ferryl Intermediate (Compound II) and Nadph Complex.

Murshudov, G.N., Grebenko, A.I., Brannigan, J.A., Antson, A.A., Barynin, V.V., Dodson, G.G., Dauter, Z., Wilson, K.S., Melik-Adamyan, W.R.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1972-1982

• PubMed: 12454454 
• DOI: 10.1107/s0907444902016566
• Primary Citation of Related Structures:  
  1GWE, 1GWF, 1GWH


• PubMed Abstract: 
  

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.

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Organizational Affiliation: 

Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase	A	503	Micrococcus luteus	Mutation(s): 0  Gene Names: katA EC: 1.11.1.6
UniProt
Find proteins for P29422 (Micrococcus luteus) Explore P29422  Go to UniProtKB:  P29422

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.88 Å
• R-Value Free: 0.096 
• R-Value Work: 0.089 
• R-Value Observed: 0.089 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.785	α = 90
b = 105.785	β = 90
c = 105.001	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-15 
• Released Date: 2002-04-26 
Deposition Author(s): Murshudov, G.N., Grebenko, A.I., Brannigan, J.A., Antson, A.A., Barynin, V.V., Dodson, G.G., Dauter, Z., Wilson, K.S., Melik-Adamyan, W.R.

Revision History  

• Version 1.0: 2002-04-26
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
• Version 1.2: 2018-06-20
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.3: 2019-07-10
  Changes: Data collection
• Version 1.4: 2019-07-24
  Changes: Data collection