4E5K | pdb_00004e5k

Thermostable phosphite dehydrogenase in complex with NAD and sulfite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.267 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.219 (Depositor) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 146.62 kDa 
  • Atom Count: 10,830 
  • Modeled Residue Count: 1,315 
  • Deposited Residue Count: 1,316 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphite dehydrogenase (thermostable variant)
A, B, C, D
329Stutzerimonas stutzeriMutation(s): 0 
EC: 1.20.1.1
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

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
L [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO3

Query on SO3



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
K [auth D]
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.267 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.219 (Depositor) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.06α = 90
b = 114.18β = 112.33
c = 88.31γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



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, Source and taxonomy
  • Version 1.2: 2020-02-26
    Changes: Data collection
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description