1NPX

STRUCTURE OF NADH PEROXIDASE FROM STREPTOCOCCUS FAECALIS 10C1 REFINED AT 2.16 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of NADH peroxidase from Streptococcus faecalis 10C1 refined at 2.16 A resolution.

Stehle, T.Ahmed, S.A.Claiborne, A.Schulz, G.E.

(1991) J.Mol.Biol. 221: 1325-1344


  • PubMed Abstract: 
  • The crystal structure of NADH peroxidase (EC 1.11.1.1) from Streptococcus faecalis 10C1 (Enterococcus faecalis) has been refined to a resolution of 2.16 A using the simulated annealing method. The final crystallographic R-factor is 17.7% for all data ...

    The crystal structure of NADH peroxidase (EC 1.11.1.1) from Streptococcus faecalis 10C1 (Enterococcus faecalis) has been refined to a resolution of 2.16 A using the simulated annealing method. The final crystallographic R-factor is 17.7% for all data in the resolution range 7 to 2.16 A. The standard deviations are 0.015 A in bond lengths and 3.0 degrees in bond angles for the final model, which includes all 447 amino acid residues, one FAD and 369 water molecules. The enzyme is a symmetrical tetramer with point group D2; the symmetry is crystallographic. The redox center of the enzyme consists of FAD and a cysteine (Cys42), which forms a sulfenic acid (Cys-SOH) in its oxidized state. A histidine (His10) close to Cys42 is likely to act as an active-site base. In the analyzed crystal, the enzyme was in a non-native oxidation state with Cys42 oxidized to a sulfonic acid Cys-SO3H. The chain fold of NADH peroxidase is similar to those of disulfide oxidoreductases. A comparison with glutathione reductase, a representative of this enzyme family, is given.


    Related Citations: 
    • The Non-Flavin Redox Center of the Streptococcal Nadh Peroxidase. II. Evidence for a Stabilized Cysteine-Sulfenic Acid
      Poole, L.B.,Claiborne, A.
      (1989) J.Biol.Chem. 264: 12330
    • Interactions of Pyridine Nucleotides with Redox Forms of the Flavin-Containing Nadh Peroxidase from Streptococcus Faecalis
      Poole, L.B.,Claiborne, A.
      (1986) J.Biol.Chem. 261: 14525
    • The Structure of Nadh Peroxidase from Streptococcus Faecalis at 3.3 Angstroms Resolution
      Stehle, T.,Ahmed, S.A.,Claiborne, A.,Schulz, G.E.
      (1990) FEBS Lett. 267: 186
    • Cloning, Sequence and Overexpression of Nadh Peroxidase from Streptococcus Faecalis 10C1. Structural Relationship with the Flavoprotein Disulfide Reductases
      Ross, R.P.,Claiborne, A.
      (1991) J.Mol.Biol. 221: 857
    • The Non-Flavin Redox Center of the Streptococcal Nadh Peroxidase. I. Thiol Reactivity and Redox Behavior in the Presence of Urea
      Poole, L.B.,Claiborne, A.
      (1989) J.Biol.Chem. 264: 12322


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie der Universität, Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH PEROXIDASE
A
447Enterococcus faecalis (strain ATCC 700802 / V583)Gene Names: npr
EC: 1.11.1.1
Find proteins for P37062 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  P37062
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Work: 0.177 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 77.200α = 90.00
b = 134.500β = 90.00
c = 145.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance