Histamine dehydrogenase from Nocardiodes simplex

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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Crystal structure of histamine dehydrogenase from Nocardioides simplex.

Reed, T.Lushington, G.H.Xia, Y.Hirakawa, H.Travis, D.M.Mure, M.Scott, E.E.Limburg, J.

(2010) J Biol Chem 285: 25782-25791

  • DOI: https://doi.org/10.1074/jbc.M109.084301
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Histamine dehydrogenase (HADH) isolated from Nocardioides simplex catalyzes the oxidative deamination of histamine to imidazole acetaldehyde. HADH is highly specific for histamine, and we are interested in understanding the recognition mode of histamine in its active site. We describe the first crystal structure of a recombinant form of HADH (HADH) to 2.7-A resolution. HADH is a homodimer, where each 76-kDa subunit contains an iron-sulfur cluster ([4Fe-4S](2+)) and a 6-S-cysteinyl flavin mononucleotide (6-S-Cys-FMN) as redox cofactors. The overall structure of HADH is very similar to that of trimethylamine dehydrogenase (TMADH) from Methylotrophus methylophilus (bacterium W3A1). However, some distinct differences between the structure of HADH and TMADH have been found. Tyr(60), Trp(264), and Trp(355) provide the framework for the "aromatic bowl" that serves as a trimethylamine-binding site in TMADH is comprised of Gln(65), Trp(267), and Asp(358), respectively, in HADH. The surface Tyr(442) that is essential in transferring electrons to electron-transfer flavoprotein (ETF) in TMADH is not conserved in HADH. We use this structure to propose the binding mode for histamine in the active site of HADH through molecular modeling and to compare the interactions to those observed for other histamine-binding proteins whose structures are known.

  • Organizational Affiliation

    Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine dehydrogenase
A, B
690Pimelobacter simplexMutation(s): 0 
Gene Names: hadhhdh
Find proteins for Q6IWJ5 (Nocardioides simplex)
Explore Q6IWJ5 
Go to UniProtKB:  Q6IWJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IWJ5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.141α = 90
b = 107.035β = 90
c = 153.352γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata 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: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description