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


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.USA 98: 14268-14273

  • DOI: 10.1073/pnas.241429098

  • 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 ( ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
QUINOHEMOPROTEIN AMINE DEHYDROGENASE
A
489Paracoccus denitrificansN/A
Find proteins for Q8VUT0 (Paracoccus denitrificans)
Go to UniProtKB:  Q8VUT0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
QUINOHEMOPROTEIN AMINE DEHYDROGENASE
B
337Paracoccus denitrificansN/A
Find proteins for Q8VUS7 (Paracoccus denitrificans)
Go to UniProtKB:  Q8VUS7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
QUINOHEMOPROTEIN AMINE DEHYDROGENASE
C
79Paracoccus denitrificansGene Names: qhnDH
EC: 1.4.99.-
Find proteins for Q8VUS8 (Paracoccus denitrificans)
Go to UniProtKB:  Q8VUS8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
TBU
Query on TBU

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Download CCD File 
A, B, C
TERTIARY-BUTYL ALCOHOL
2-METHYL-2-PROPANOL
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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 = 90.00
b = 99.489β = 90.00
c = 214.489γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SOLVEphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance