8CAT

The NADPH binding site on beef liver catalase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

The NADPH binding site on beef liver catalase.

Fita, I.Rossmann, M.G.

(1985) Proc.Natl.Acad.Sci.USA 82: 1604-1608

  • Primary Citation of Related Structures:  

  • 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 polypep ...

    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.


    Related Citations: 
    • The Active Center of Catalase
      Fita, I.,Rossmann, M.G.
      (1985) J.Mol.Biol. 185: 21
    • Structure and Heme Environment of Beef Liver Catalase at 2.5 Angstroms Resolution
      Reid III, T.J.,Murthy, M.R.N.,Sicignano, A.,Tanaka, N.,Musick, W.D.L.,Rossmann, M.G.
      (1981) Proc.Natl.Acad.Sci.USA 78: 4767
    • The Structure of Beef Liver Catalase
      Murthy, M.R.N.,Reid III, T.J.,Sicignano, A.,Tanaka, N.,Rossmann, M.G.
      (1981) Kristallografiya 26: 1017
    • The Structure of Beef Liver Catalase
      Murthy, M.R.N.,Reid III, T.J.,Sicignano, A.,Tanaka, N.,Rossmann, M.G.
      (1981) Sov.Phys.Crystallogr.(Engl.Transl.) 26: 577
    • The Refined Structure of Beef Liver Catalase at 2.5 Angstroms Resolution
      Fita, I.,Silva, A.M.,Murthy, M.R.N.,Rossmann, M.G.
      (1986) Acta Crystallogr.,Sect.B 42: 497
    • Structure of Beef Liver Catalase
      Murthy, M.R.N.,Reid III, T.J.,Sicignano, A.,Tanaka, N.,Rossmann, M.G.
      (1981) J.Mol.Biol. 152: 465
    • Crystalline Bovine Liver Catalase
      Eventoff, W.,Tanaka, N.,Rossmann, M.G.
      (1976) J.Mol.Biol. 103: 799
    • Comparison of Beef Liver and Penicillium Vitale Catalases
      Melik-Adamyan, W.R.,Barynin, V.V.,Vagin, A.A.,Borisov, V.V.,Vainshtein, B.K.,Fita, I.,Murthy, M.R.N.,Rossmann, M.G.
      (1986) J.Mol.Biol. 188: 63
    • The Molecular Symmetry of Bovine Liver Catalase
      Eventoff, W.,Gurskaya, G.V.
      (1975) J.Mol.Biol. 93: 55



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATALASE
A, B
506Bos taurusMutation(s): 0 
Gene Names: CAT
EC: 1.11.1.6
Find proteins for P00432 (Bos taurus)
Go to Gene View: CAT
Go to UniProtKB:  P00432
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NDPKd: <10 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.191 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.000α = 90.00
b = 142.000β = 90.00
c = 103.700γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1985-04-01
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2011-10-05
    Type: Derived calculations
  • Version 1.4: 2012-11-21
    Type: Derived calculations
  • Version 1.5: 2017-11-01
    Type: Derived calculations, Other