1F8W

CRYSTAL STRUCTURE OF NADH PEROXIDASE MUTANT: R303M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Analysis of the kinetic and redox properties of the NADH peroxidase R303M mutant: correlation with the crystal structure.

Crane III, E.J.Yeh, J.I.Luba, J.Claiborne, A.

(2000) Biochemistry 39: 10353-10364


  • PubMed Abstract: 
  • The crystal structure of the flavoprotein NADH peroxidase shows that the Arg303 side chain forms a hydrogen bond with the active-site His10 imidazole and is therefore likely to influence the catalytic mechanism. Dithionite titration of an R303M mutan ...

    The crystal structure of the flavoprotein NADH peroxidase shows that the Arg303 side chain forms a hydrogen bond with the active-site His10 imidazole and is therefore likely to influence the catalytic mechanism. Dithionite titration of an R303M mutant [E(FAD, Cys42-sulfenic acid)] yields a two-electron reduced intermediate (EH(2)) with enhanced flavin fluorescence and almost no charge-transfer absorbance at pH 7.0; the pK(a) for the nascent Cys42-SH is increased by over 3.5 units in comparison with the wild-type EH(2) pK(a) of Cys42-SOH. The crystal structure of the R303M peroxidase has been refined at 2.45 A resolution. In addition to eliminating the Arg303 interactions with His10 and Glu14, the mutant exhibits a significant change in the conformation of the Cys42-SOH side chain relative to FAD and His10 in particular. These and other results provide a detailed understanding of Arg303 and its role in the structure and mechanism of this unique flavoprotein peroxidase.


    Related Citations: 
    • Structure of the Native Cysteine-sulfenic Acid Redox Center of Enterococcal NADH Peroxidase Refined at 2.8 A Resolution
      Yeh, J.I.,Claiborne, A.,Hol, W.G.
      (1996) Biochemistry 35: 9951


    Organizational Affiliation

    Department of Biochemistry, Wake Forest University Medical Center, Winston-Salem, North Carolina 27157, 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 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
CSX
Query on CSX
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 155.180α = 90.00
b = 155.180β = 90.00
c = 189.410γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-01-24
    Type: Database references
  • Version 1.4: 2018-01-31
    Type: Database references