1JQE

Crystal Structure Analysis of Human Histamine Methyltransferase (Ile105 Polymorphic Variant) Complexed with AdoHcy and Antimalarial Drug Quinacrine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1016/s0969-2126(01)00643-8
  • Primary Citation of Related Structures:  
    1JQD, 1JQE

  • 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 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. Two ternary structures of human HNMT have been determined: the Thr105 variant complexed with its substrate histamine and reaction product AdoHcy and the Ile105 variant complexed with an inhibitor (quinacrine) and AdoHcy. Our steady-state kinetic data indicate that the recombinant Ile105 variant shows 1.8- and 1.3-fold increases in the apparent K(M) for AdoMet and histamine, respectively, and slightly (16%) but consistently lower specific activity as compared to that of the Thr105 variant. These differences hold over a temperature range of 25 degrees C-45 degrees C in vitro. Only at a temperature of 50 degrees C or higher is the Ile105 variant more thermolabile than the Thr105 enzyme. HNMT has a 2 domain structure including a consensus AdoMet binding domain, where the residue 105 is located on the surface, consistent with the kinetic data that the polymorphism does not affect overall protein stability at physiological temperatures but lowers K(M) values for AdoMet and histamine. The interactions between HNMT and quinacrine provide the first structural insights into a large group of pharmacologic HNMT inhibitors and their mechanisms of inhibition.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine N-Methyltransferase
A, B
292Homo sapiensMutation(s): 1 
Gene Names: HNMT
EC: 2.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P50135 (Homo sapiens)
Explore P50135 
Go to UniProtKB:  P50135
PHAROS:  P50135
GTEx:  ENSG00000150540 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50135
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QUN
Query on QUN

Download Ideal Coordinates CCD File 
D [auth A]QUINACRINE
C23 H30 Cl N3 O
GPKJTRJOBQGKQK-MRXNPFEDSA-N
SAH
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
F [auth B]
G [auth B]
H [auth B]
I [auth B]
J [auth B]
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
UNKNOWN ATOM OR ION
X
Binding Affinity Annotations 
IDSourceBinding Affinity
QUN PDBBind:  1JQE Ki: 360 (nM) from 1 assay(s)
SAH BindingDB:  1JQE Ki: 1.81e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.34α = 90
b = 130.34β = 90
c = 63.01γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-04-03
    Changes: Refinement description