4EBF

SeMet thermostable phosphite dehydrogenase Glu175-Ala mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of phosphite dehydrogenase provide insights into nicotinamide cofactor regeneration.

Zou, Y.Zhang, H.Brunzelle, J.S.Johannes, T.W.Woodyer, R.Hung, J.E.Nair, N.van der Donk, W.A.Zhao, H.Nair, S.K.

(2012) Biochemistry 51: 4263-4270

  • DOI: https://doi.org/10.1021/bi2016926
  • Primary Citation of Related Structures:  
    4E5K, 4E5M, 4E5N, 4E5P, 4EBF

  • PubMed Abstract: 

    The enzyme phosphite dehydrogenase (PTDH) catalyzes the NAD(+)-dependent conversion of phosphite to phosphate and represents the first biological catalyst that has been shown to conduct the enzymatic oxidation of phosphorus. Despite investigation for more than a decade into both the mechanism of its unusual reaction and its utility in cofactor regeneration, there has been a lack of any structural data for PTDH. Here we present the cocrystal structure of an engineered thermostable variant of PTDH bound to NAD(+) (1.7 Å resolution), as well as four other cocrystal structures of thermostable PTDH and its variants with different ligands (all between 1.85 and 2.3 Å resolution). These structures provide a molecular framework for understanding prior mutational analysis and point to additional residues, located in the active site, that may contribute to the enzymatic activity of this highly unusual catalyst.


  • Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermostable phosphite dehydrogenase
A, B, C, D, E
A, B, C, D, E, F
334Stutzerimonas stutzeriMutation(s): 0 
Gene Names: ptx
UniProt
Find proteins for O69054 (Stutzerimonas stutzeri)
Explore O69054 
Go to UniProtKB:  O69054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO69054
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.218α = 90
b = 122.58β = 96.36
c = 135.015γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-06-13
    Changes: Database references