2NPX | pdb_00002npx

NADH BINDING SITE AND CATALYSIS OF NADH PEROXIDASE

• PDB DOI: https://doi.org/10.2210/pdb2NPX/pdb

• Classification: OXIDOREDUCTASE(H2O2(A))
• Organism(s): Enterococcus faecalis
• Mutation(s): No 


• Deposited: 1992-05-29 Released: 1994-01-31 
• Deposition Author(s): Stehle, T., Claiborne, A., Schulz, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 
  0.159 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

NADH binding site and catalysis of NADH peroxidase.

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

(1993) Eur J Biochem 211: 221-226

• PubMed: 8425532 
• DOI: https://doi.org/10.1111/j.1432-1033.1993.tb19889.x
• Primary Citation Related Structures: 
  2NPX


• PubMed Abstract: 
  

  The structure of the complex between cofactor NADH and the enzyme NADH peroxidase from Streptococcus faecalis 10C1 (Enterococcus faecalis) has been determined by crystal soaking, X-ray data collection, model building of NADH and refinement at 0.24-nm resolution based on the known enzyme structure [Stehle, T., Ahmed, S. A., Claiborne, A. & Schulz, G. E. (1991) J. Mol. Biol. 221, 1325-1344]. Apart from NADH, the catalytic center of the enzyme contains FAD and a cysteine that shuttles between thiolate and sulfenic acid states. Unfortunately, this cysteine was irreversibly oxidized to a cysteine sulfonic acid in the established enzyme structure. Based on the geometry of the catalytic center, we discuss the stabilization of the oxidation-sensitive sulfenic acid and propose a reaction mechanism.

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Organizational Affiliation: 
• Institut für Organische Chemie und Biochemie der Universität, Freiburg im Breisgau, Federal Republic of Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 51.1 kDa 
• Atom Count: 3,927 
• Modeled Residue Count: 447 
• Deposited Residue Count: 447 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH PEROXIDASE	A	447	Enterococcus faecalis	Mutation(s): 0  EC: 1.11.1.1
UniProt
Find proteins for P37062 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore P37062  Go to UniProtKB:  P37062

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAD	C [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work:  0.159 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.2	α = 90
b = 134.5	β = 90
c = 145.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Stehle, T., Claiborne, A., Schulz, G.E.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2024-06-05
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other