1NHP

CRYSTALLOGRAPHIC ANALYSES OF NADH PEROXIDASE CYS42ALA AND CYS42SER MUTANTS: ACTIVE SITE STRUCTURE, MECHANISTIC IMPLICATIONS, AND AN UNUSUAL ENVIRONMENT OF ARG303


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic analyses of NADH peroxidase Cys42Ala and Cys42Ser mutants: active site structures, mechanistic implications, and an unusual environment of Arg 303.

Mande, S.S.Parsonage, D.Claiborne, A.Hol, W.G.

(1995) Biochemistry 34: 6985-6992

  • Primary Citation of Related Structures:  1NHQ

  • PubMed Abstract: 
  • NADH peroxidase from Enterococcus faecalis is a tetrameric flavoenzyme of 201,400 Da which employs Cys 42 as a redox-active center cycling between sulfhydryl (Cys-SH) and sulfenic acid (Cys-SOH) states along the catalytic pathway. The role of the act ...

    NADH peroxidase from Enterococcus faecalis is a tetrameric flavoenzyme of 201,400 Da which employs Cys 42 as a redox-active center cycling between sulfhydryl (Cys-SH) and sulfenic acid (Cys-SOH) states along the catalytic pathway. The role of the active site cysteine 42 in NADH peroxidase has been elucidated using biochemical and crystallographic techniques. Here we describe the crystal structures of two active site cysteine mutants, Cys42Ala and Cys42Ser, which were determined to 2.0 A resolution and refined to crystallographic R values of 17.6 and 18.3%, respectively. The overall chain fold and the quaternary structure of the two mutants appear to be very similar to wild-type enzyme. Therefore, the substantially lower activity of the mutants is due to the absence of the Cys-SOH redox center. One of the oxygen atoms of the nonnative cysteine sulfonic acid in the wild-type structure is replaced by a water molecule in both mutant structures. Two other residues near the active site are His 10 and Arg 303. A detailed analysis of the environment of these residues in the mutant and wild-type peroxidase structures indicates that the imidazole ring of His 10 is uncharged. The interactions made by the guanidinium group of Arg 303 involve not only His 10 but also the carboxylate of Glu 14 and Tyr 60. Interestingly, the Nn1H function of Arg 303 is oriented perpendicular to the plane of the phenyl ring of Tyr 60 with a Nn1 to phenyl ring center distance of 3.8 A, suggesting a favorable electrostatic interaction between Arg 303 and Tyr 60.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • Structure of Nadh Peroxidase from Streptococcus Faecalis 10C1 Refined at 2.16 Angstroms
      Stehle, T.,Ahmed, S.A.,Claiborne, A.,Schulz, G.E.
      (1991) J.Mol.Biol. 221: 1325


    Organizational Affiliation

    Department of Biological Structure, School of Medicine, University of Washington, Seattle 98195, USA.




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.176 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 77.600α = 90.00
b = 134.800β = 90.00
c = 146.300γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-14
    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
  • Version 1.3: 2012-03-28
    Type: Structure summary