4E1O

Human histidine decarboxylase complex with Histidine methyl ester (HME)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M112.381897

  • 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 ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histidine decarboxylase
A, B, C, D, E, F
481Homo sapiensMutation(s): 2 
Gene Names: HDC
EC: 4.1.1.22
Find proteins for P19113 (Homo sapiens)
Go to Gene View: HDC
Go to UniProtKB:  P19113
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PVH
Query on PVH

Download SDF File 
Download CCD File 
A, B, C, D, E, F
HISTIDINE-METHYL-ESTER
C7 H12 N3 O2
BXRMEWOQUXOLDH-LURJTMIESA-O
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
A, B, C, D, E, F
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.162 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 215.163α = 90.00
b = 112.723β = 110.30
c = 171.393γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-07-25
    Type: Database references
  • Version 1.2: 2013-07-17
    Type: Database references