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 

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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: 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 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
QUINOHEMOPROTEIN AMINE DEHYDROGENASEA489Paracoccus 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
QUINOHEMOPROTEIN AMINE DEHYDROGENASEB337Paracoccus 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
QUINOHEMOPROTEIN AMINE DEHYDROGENASEC79Paracoccus denitrificansMutation(s): 0 
Gene Names: qhnDH
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
TBU
Query on TBU

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B],
I [auth C]
TERTIARY-BUTYL ALCOHOL
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-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
b = 99.489β = 90
c = 214.489γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata 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: 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