2PIA

PHTHALATE DIOXYGENASE REDUCTASE: A MODULAR STRUCTURE FOR ELECTRON TRANSFER FROM PYRIDINE NUCLEOTIDES TO [2FE-2S]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Phthalate dioxygenase reductase: a modular structure for electron transfer from pyridine nucleotides to [2Fe-2S].

Correll, C.C.Batie, C.J.Ballou, D.P.Ludwig, M.L.

(1992) Science 258: 1604-1610

  • DOI: https://doi.org/10.1126/science.1280857
  • Primary Citation of Related Structures:  
    2PIA

  • PubMed Abstract: 

    Phthalate dioxygenase reductase (PDR) is a prototypical iron-sulfur flavoprotein (36 kilodaltons) that utilizes flavin mononucleotide (FMN) to mediate electron transfer from the two-electron donor, reduced nicotinamide adenine nucleotide (NADH), to the one-electron acceptor, [2Fe-2S]. The crystal structure of oxidized PDR from Pseudomonas cepacia has been analyzed at 2.0 angstrom resolution resolution; reduced PDR and pyridine nucleotide complexes have been analyzed at 2.7 angstrom resolution. NADH, FMN, and the [2Fe-2S] cluster, bound to distinct domains, are brought together near a central cleft in the molecule, with only 4.9 angstroms separating the flavin 8-methyl and a cysteine sulfur ligated to iron. The domains that bind FMN and [2Fe-2S] are packed so that the flavin ring and the plane of the [2Fe-2S] core are approximately perpendicular. The [2Fe-2S] group is bound by four cysteines in a site resembling that in plant ferredoxins, but its redox potential (-174 millivolts at pH 7.0) is much higher than the potentials of plant ferredoxins. Structural and sequence similarities assign PDR to a distinct family of flavoprotein reductases, all related to ferredoxin NADP(+)-reductase.


  • Organizational Affiliation

    Department of Biological Chemistry and Biophysics, University of Michigan, Ann Arbor 48109.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHTHALATE DIOXYGENASE REDUCTASE321Burkholderia cepaciaMutation(s): 0 
EC: 1.18.1
UniProt
Find proteins for P33164 (Burkholderia cepacia)
Explore P33164 
Go to UniProtKB:  P33164
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33164
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
C [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.186 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.4α = 90
b = 114.4β = 90
c = 77.8γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-04-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Advisory, Derived calculations, Other
  • Version 1.4: 2024-02-21
    Changes: Advisory, Data collection, Database references, Derived calculations