Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 339.57 kDa 
• Atom Count: 25,850 
• Modelled Residue Count: 2,908 
• Deposited Residue Count: 3,012 
• Unique protein chains: 1

 1CF9

Structure of the mutant VAL169CYS of catalase HPII from Escherichia coli

• PDB DOI:  https://doi.org/10.2210/pdb1CF9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-03-24 Released: 1999-04-06 
• Deposition Author(s): Mate, M.J., Loewen, P.C., Fita, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.181 

Literature

Mutants that alter the covalent structure of catalase hydroperoxidase II from Escherichia coli.

Mate, M.J., Sevinc, M.S., Hu, B., Bujons, J., Bravo, J., Switala, J., Ens, W., Loewen, P.C., Fita, I.

(1999) J Biol Chem 274: 27717-27725

• PubMed: 10488114 
• DOI: https://doi.org/10.1074/jbc.274.39.27717
• Primary Citation of Related Structures:  
  1CF9, 1QF7


• PubMed Abstract: 
  

The three-dimensional structures of two HPII variants, V169C and H392Q, have been determined at resolutions of 1.8 and 2.1 A, respectively. The V169C variant contains a new type of covalent bond between the sulfur atom of Cys(169) and a carbon atom on the imidazole ring of the essential His(128). This variant enzyme has only residual catalytic activity and contains heme b. The chain of water molecules visible in the main channel may reflect the organization of the hydrogen peroxide substrates in the active enzyme. Two alternative mechanisms, involving either compound I or free radical intermediates, are presented to explain the formation of the Cys-His covalent bond. The H392Q and H392E variants exhibit 75 and 25% of native catalytic activity, respectively. The Gln(392) variant contains only heme b, whereas the Glu(392) variant contains a mixture of heme b and cis and trans isomers of heme d, suggesting of a role for this residue in heme conversion. Replacement of either Gln(419) and Ser(414), both of which interact with the heme, affected the cis:trans ratio of spirolactone heme d. Implications for the heme oxidation mechanism and the His-Tyr bond formation in HPII are considered.

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Related Citations: 

• Crystal Structure of Catalase HPII from Escherichia Coli
  Bravo, J., Verdaguer, N., Tormo, J., Betzel, C., Switala, J., Loewen, P.C., Fita, I.
  (1995) Structure 3: 491

• 2.8 A Crystal Structure of Catalase Hpii from Escherichia Coli
  Bravo, J., Tormo, J., Verdaguer, N., Fita, I., Betzel, C., Switala, J., Loewen, P.C.
  (1993) Acta Crystallogr A 28: 79

• Crystallization and Preliminary X-Ray Diffraction Analysis of Catalase Hpii from Escherichia Coli
  Tormo, J., Fita, I., Switala, J., Loewen, P.C.
  (1990) J Mol Biol 213: 219

• The Refined Structure of Beef Liver Catalase at 2.5 A Resolution
  Fita, I., Silva, A.M., Murthy, M.R.N., Rossmann, M.G.
  (1986) Acta Crystallogr B 42: 497

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Organizational Affiliation: 

CID (Consejo Superior de Investigaciones Cietifícas) Jordi Girona 18-26, 08034 Barcelona, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CATALASE HPII)	A, B, C, D	753	Escherichia coli	Mutation(s): 1  EC: 1.11.1.6
UniProt
Find proteins for P21179 (Escherichia coli (strain K12)) Explore P21179  Go to UniProtKB:  P21179

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], F [auth B], G [auth C], H [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.47	α = 90
b = 133.04	β = 109.64
c = 122.22	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-06 
Deposition Author(s): Mate, M.J., Loewen, P.C., Fita, I.

Revision History  

• Version 1.0: 1999-04-06
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2014-03-12
  Changes: Database references, Structure summary
• Version 1.4: 2018-03-14
  Changes: Data collection, Database references