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 

wwPDB Validation 3D Report Full Report


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

  • 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 sev ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Amine DehydrogenaseA494Pseudomonas putidaMutation(s): 0 
Find proteins for Q8VW85 (Pseudomonas putida)
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Go to UniProtKB:  Q8VW85
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Amine DehydrogenaseB349Pseudomonas putidaMutation(s): 0 
Find proteins for Q8VW82 (Pseudomonas putida)
Explore Q8VW82 
Go to UniProtKB:  Q8VW82
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Amine DehydrogenaseG79Pseudomonas putidaMutation(s): 0 
Gene Names: qhnDH
EC: 1.4.99
Find proteins for P0A182 (Pseudomonas putida)
Explore P0A182 
Go to UniProtKB:  P0A182
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC
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A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N		 Ligand Interaction
NI
Query on NI
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A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TRQ
Query on TRQ		GL-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 

  • 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