1JJU

Structure of a Quinohemoprotein Amine Dehydrogenase with a Unique Redox Cofactor and Highly Unusual Crosslinking


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking.

Datta, S.Mori, Y.Takagi, K.Kawaguchi, K.Chen, Z.W.Okajima, T.Kuroda, S.Ikeda, T.Kano, K.Tanizawa, K.Mathews, F.S.

(2001) Proc Natl Acad Sci U S A 98: 14268-14273

  • DOI: https://doi.org/10.1073/pnas.241429098
  • Primary Citation of Related Structures:  
    1JJU

  • PubMed Abstract: 

    The crystal structure of the heterotrimeric quinohemoprotein amine dehydrogenase from Paracoccus denitrificans has been determined at 2.05-A resolution. Within an 82-residue subunit is contained an unusual redox cofactor, cysteine tryptophylquinone (CTQ), consisting of an orthoquinone-modified tryptophan side chain covalently linked to a nearby cysteine side chain. The subunit is surrounded on three sides by a 489-residue, four-domain subunit that includes a diheme cytochrome c. Both subunits sit on the surface of a third subunit, a 337-residue seven-bladed beta-propeller that forms part of the enzyme active site. The small catalytic subunit is internally crosslinked by three highly unusual covalent cysteine to aspartic or glutamic acid thioether linkages in addition to the cofactor crossbridge. The catalytic function of the enzyme as well as the biosynthesis of the unusual catalytic subunit is discussed.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
QUINOHEMOPROTEIN AMINE DEHYDROGENASE489Paracoccus denitrificansMutation(s): 0 
UniProt
Find proteins for Q8VUT0 (Paracoccus denitrificans)
Explore Q8VUT0 
Go to UniProtKB:  Q8VUT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VUT0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
QUINOHEMOPROTEIN AMINE DEHYDROGENASE337Paracoccus denitrificansMutation(s): 0 
UniProt
Find proteins for Q8VUS7 (Paracoccus denitrificans)
Explore Q8VUS7 
Go to UniProtKB:  Q8VUS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VUS7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
QUINOHEMOPROTEIN AMINE DEHYDROGENASE79Paracoccus denitrificansMutation(s): 0 
EC: 1.4.2
UniProt
Find proteins for Q8VUS8 (Paracoccus denitrificans)
Explore Q8VUS8 
Go to UniProtKB:  Q8VUS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VUS8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TRQ
Query on TRQ
C
L-PEPTIDE LINKINGC11 H10 N2 O4TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.489α = 90
b = 99.489β = 90
c = 214.489γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata 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: 2001-12-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance