Human histidine decarboxylase complex with Histidine methyl ester (HME)

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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This is version 2.0 of the entry. See complete history


Structural study reveals that Ser-354 determines substrate specificity on human histidine decarboxylase

Komori, H.Nitta, Y.Ueno, H.Higuchi, Y.

(2012) J Biol Chem 287: 29175-29183

  • DOI: https://doi.org/10.1074/jbc.M112.381897
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Histamine is an important chemical mediator for a wide variety of physiological reactions. L-histidine decarboxylase (HDC) is the primary enzyme responsible for histamine synthesis and produces histamine from histidine in a one-step reaction. In this study, we determined the crystal structure of human HDC (hHDC) complexed with the inhibitor histidine methyl ester. This structure shows the detailed features of the pyridoxal-5'-phosphate inhibitor adduct (external aldimine) at the active site of HDC. Moreover, a comparison of the structures of hHDC and aromatic L-amino acid (L-DOPA) decarboxylase showed that Ser-354 was a key residue for substrate specificity. The S354G mutation at the active site enlarged the size of the hHDC substrate-binding pocket and resulted in a decreased affinity for histidine, but an acquired ability to bind and act on L-DOPA as a substrate. These data provide insight into the molecular basis of substrate recognition among the group II pyridoxal-5'-phosphate-dependent decarboxylases.

  • Organizational Affiliation

    Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan. komori@sci.u-hyogo.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histidine decarboxylase
A, B, C, D, E
A, B, C, D, E, F
481Homo sapiensMutation(s): 2 
Gene Names: HDC
UniProt & NIH Common Fund Data Resources
Find proteins for P19113 (Homo sapiens)
Explore P19113 
Go to UniProtKB:  P19113
GTEx:  ENSG00000140287 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19113
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLP

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
C8 H10 N O6 P
Query on PVH

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
C7 H12 N3 O2
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CSX
A, B, C, D, E
A, B, C, D, E, F
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 215.163α = 90
b = 112.723β = 110.3
c = 171.393γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2013-07-17
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations