7CAT | pdb_00007cat

The NADPH binding site on beef liver catalase

• PDB DOI: https://doi.org/10.2210/pdb7CAT/pdb
• Entry: 7CAT supersedes: 3CAT

• Classification: OXIDOREDUCTASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 1984-11-15 Released: 1985-04-01 
• Deposition Author(s): Murthy, M.R.N., Reid III, T.J., Sicignano, A., Tanaka, N., Fita, I., Rossmann, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.212 (Depositor) 

Literature

The NADPH binding site on beef liver catalase.

Fita, I., Rossmann, M.G.

(1985) Proc Natl Acad Sci U S A 82: 1604-1608

• PubMed: 3856839 
• DOI: https://doi.org/10.1073/pnas.82.6.1604
• Primary Citation Related Structures: 
  7CAT, 8CAT


• PubMed Abstract: 
  

  Beef liver and human erythrocyte catalases (EC 1.11.1.6) bind NADP tenaciously [Kirkman, H. N. & Gaetani, G. F. (1984) Proc. Natl. Acad. Sci. USA 81, 4343-4348]. The position of NADP on beef liver catalase corresponds to the carboxyl-terminal polypeptide hinge in Penicillium vitale fungal catalase, which connects the common catalase structure to the additional flavodoxin-like domain. In contrast to nearly all other known structures of protein-bound NADP, NAD, and FAD, the NADP molecule of beef liver catalase is folded into a right-handed helix and bound, in part, in the vicinity of the carboxyl end of two alpha-helices. A water molecule (W7) occupies a pseudosubstrate site close to the C4 position of the nicotinamide and is hydrogen bonded to His-304. Although the NADP and heme groups approach each other to within 13.7 A, there is no direct interaction. The function of the NADP remains a mystery.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 118.05 kDa 
• Atom Count: 8,298 
• Modeled Residue Count: 996 
• Deposited Residue Count: 1,012 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATALASE	A, B	506	Bos taurus	Mutation(s): 0  EC: 1.11.1.6
UniProt
Find proteins for P00432 (Bos taurus) Explore P00432  Go to UniProtKB:  P00432

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	D [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.212 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142	α = 90
b = 142	β = 90
c = 103.7	γ = 120

Structure Validation

Entry History 

Deposition Data

• Released Date: 1985-04-01 
Deposition Author(s): Murthy, M.R.N., Reid III, T.J., Sicignano, A., Tanaka, N., Fita, I., Rossmann, M.G.
• This entry supersedes: 3CAT

Revision History  

• Version 1.0: 1985-04-01
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2011-10-12
  Changes: Derived calculations
• Version 1.4: 2012-11-21
  Changes: Derived calculations
• Version 2.0: 2023-09-27
  Type: Remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description