1JMX

crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.209 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of quinohemoprotein amine dehydrogenase from Pseudomonas putida. Identification of a novel quinone cofactor encaged by multiple thioether cross-bridges.

Satoh, A.Kim, J.K.Miyahara, I.Devreese, B.Vandenberghe, I.Hacisalihoglu, A.Okajima, T.Kuroda, S.Adachi, O.Duine, J.A.Van Beeumen, J.Tanizawa, K.Hirotsu, K.

(2002) J Biol Chem 277: 2830-2834

  • DOI: https://doi.org/10.1074/jbc.M109090200
  • Primary Citation of Related Structures:  
    1JMX, 1JMZ

  • PubMed Abstract: 

    The crystal structure of a quinohemoprotein amine dehydrogenase from Pseudomonas putida has been determined at 1.9-A resolution. The enzyme comprises three non-identical subunits: a four-domain alpha-subunit that harbors a di-heme cytochrome c, a seven-bladed beta-propeller beta-subunit that provides part of the active site, and a small gamma-subunit that contains a novel cross-linked, proteinous quinone cofactor, cysteine tryptophylquinone. More surprisingly, the catalytic gamma-subunit contains three additional chemical cross-links that encage the cysteine tryptophylquinone cofactor, involving a cysteine side chain bridged to either an Asp or Glu residue all in a hitherto unknown thioether bonding with a methylene carbon atom of acidic amino acid side chains. Thus, the structure of the 79-residue gamma-subunit is quite unusual, containing four internal cross-links in such a short polypeptide chain that would otherwise be difficult to fold into a globular structure.


  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amine Dehydrogenase494Pseudomonas putidaMutation(s): 0 
UniProt
Find proteins for Q8VW85 (Pseudomonas putida)
Explore Q8VW85 
Go to UniProtKB:  Q8VW85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VW85
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Amine Dehydrogenase349Pseudomonas putidaMutation(s): 0 
UniProt
Find proteins for Q8VW82 (Pseudomonas putida)
Explore Q8VW82 
Go to UniProtKB:  Q8VW82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VW82
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Amine DehydrogenaseC [auth G]79Pseudomonas putidaMutation(s): 0 
UniProt
Find proteins for P0A182 (Pseudomonas putida)
Explore P0A182 
Go to UniProtKB:  P0A182
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A182
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
D [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TRQ
Query on TRQ
C [auth G]L-PEPTIDE LINKINGC11 H10 N2 O4TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.21α = 90
b = 92.37β = 112
c = 79.3γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-01-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance