1JQD

Crystal Structure Analysis of Human Histamine Methyltransferase (Thr105 Polymorphic Variant) Complexed with AdoHcy and Histamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Two polymorphic forms of human histamine methyltransferase: structural, thermal, and kinetic comparisons.

Horton, J.R.Sawada, K.Nishibori, M.Zhang, X.Cheng, X.

(2001) Structure 9: 837-849

  • DOI: 10.1016/s0969-2126(01)00643-8
  • Primary Citation of Related Structures:  
    1JQE, 1JQD

  • PubMed Abstract: 
  • Histamine plays important biological roles in cell-to-cell communication; it is a mediator in allergic responses, a regulator of gastric acid secretion, a messenger in bronchial asthma, and a neurotransmitter in the central nervous system. Histamine ...

    Histamine plays important biological roles in cell-to-cell communication; it is a mediator in allergic responses, a regulator of gastric acid secretion, a messenger in bronchial asthma, and a neurotransmitter in the central nervous system. Histamine acts by binding to histamine receptors, and its local action is terminated primarily by methylation. Human histamine N-methyltransferase (HNMT) has a common polymorphism at residue 105 that correlates with the high- (Thr) and low- (Ile) activity phenotypes.


    Related Citations: 
    • Histamine N-methyltransferase pharmacogenetics: association of a common functional polymorphism with asthma
      Yan, L., Galinsky, R.E., Bernstein, J.A., Liggett, S.B., Weinshilboum, R.M.
      (2000) Pharmacogenetics 10: 261
    • Methylation pharmacogenetics: catechol O-methyltransferase, thiopurine methyltransferase, and histamine N-methyltransferase
      Weinshilboum, R.M., Otterness, D.M., Szumlanski, C.L.
      (1999) Annu Rev Pharmacol Toxicol 39: 19
    • Human histamine N-methyltransferase gene: structural characterization and chromosomal location
      Aksoy, S., Raftogianis, R., Weinshilboum, R.M.
      (1996) Biochem Biophys Res Commun 219: 548

    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histamine N-MethyltransferaseAB292Homo sapiensMutation(s): 0 
Gene Names: HNMT
EC: 2.1.1.8
Find proteins for P50135 (Homo sapiens)
Explore P50135 
Go to UniProtKB:  P50135
NIH Common Fund Data Resources
PHAROS  P50135
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
HSM
Query on HSM

Download CCD File 
A, B
HISTAMINE
C5 H9 N3
NTYJJOPFIAHURM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAHKi:  18100   nM  BindingDB
SAHKi:  10500   nM  BindingDB
SAHKi:  6900   nM  Binding MOAD
SAHKi :  6900   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.211 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.75α = 90
b = 131.75β = 90
c = 64.03γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description