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- PDB-1jqe: Crystal Structure Analysis of Human Histamine Methyltransferase (... -

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Basic information

Entry
Database: PDB / ID: 1jqe
TitleCrystal Structure Analysis of Human Histamine Methyltransferase (Ile105 Polymorphic Variant) Complexed with AdoHcy and Antimalarial Drug Quinacrine
ComponentsHistamine N-Methyltransferase
KeywordsTRANSFERASE / Classic methyltransferase fold / protein-substrate-cofactor complex / polymorphic variant
Function / homology
Function and homology information


histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome ...histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome / extracellular exosome / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Histamine N-methyltransferase-like / Histamine N-methyltransferase (EC 2.1.1.8) family profile. / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
QUINACRINE / S-ADENOSYL-L-HOMOCYSTEINE / Histamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.91 Å
AuthorsHorton, J.R. / Sawada, K. / Nishibori, M. / Zhang, X. / Cheng, X.
Citation
Journal: Structure / Year: 2001
Title: Two polymorphic forms of human histamine methyltransferase: structural, thermal, and kinetic comparisons.
Authors: Horton, J.R. / Sawada, K. / Nishibori, M. / Zhang, X. / Cheng, X.
#1: Journal: Pharmacogenetics / Year: 2000
Title: Histamine N-methyltransferase pharmacogenetics: association of a common functional polymorphism with asthma
Authors: Yan, L. / Galinsky, R.E. / Bernstein, J.A. / Liggett, S.B. / Weinshilboum, R.M.
#2: Journal: ANNU.REV.PHARMACOL.TOXICOL. / Year: 1999
Title: Methylation pharmacogenetics: catechol O-methyltransferase, thiopurine methyltransferase, and histamine N-methyltransferase
Authors: Weinshilboum, R.M. / Otterness, D.M. / Szumlanski, C.L.
#3: Journal: Biochem.Biophys.Res.Commun. / Year: 1996
Title: Human histamine N-methyltransferase gene: structural characterization and chromosomal location
Authors: Aksoy, S. / Raftogianis, R. / Weinshilboum, R.M.
History
DepositionAug 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 600HETEROGEN The density for the QUN molecule associated with monomer B is not very good. However, ...HETEROGEN The density for the QUN molecule associated with monomer B is not very good. However, some density in this region was modelled and these atoms were labelled as residue UNX, atom type UNK. Based on the QUN associated with monomer A, atoms UNX 150, 151, 152, and 376 are where the aromatic rings of a QUN could be. Atoms UNX 133 and 134 are where the amide tail of QUN could be. UNX 149 is where the side chain of B Tyr 15 could be.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histamine N-Methyltransferase
B: Histamine N-Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,85912
Polymers66,6902
Non-polymers1,16910
Water6,792377
1
A: Histamine N-Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1293
Polymers33,3451
Non-polymers7842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histamine N-Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7299
Polymers33,3451
Non-polymers3848
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.340, 130.340, 63.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Histamine N-Methyltransferase / HNMT / HMT


Mass: 33345.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNMT / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P50135, histamine N-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-QUN / QUINACRINE / 6-CHLORO-9-[[4-(DIETHYLAMINO)-1-METHYLBUTYL]AMINO]-2-METHOXYACRIDINE


Mass: 399.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30ClN3O / Comment: medication*YM
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: PEG 8000, sodium phosphate, citric acid, sodium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %PEG80001reservoir
2100 mMphosphate citrate1reservoirpH4.2
3200 mM1reservoirNaCl
415-20 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: May 17, 2000
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.91→25 Å / Num. all: 214586 / Num. obs: 202140 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 38.1
Reflection shellResolution: 1.91→1.94 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3 / Num. unique all: 1036 / % possible all: 43.8
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 44743 / Num. measured all: 202140 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 43.8 % / Num. unique obs: 946 / Num. measured obs: 4447 / Rmerge(I) obs: 0.213

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Partially refined 3.3A SeMet HNMT/AdoMet/Histamine structure solved by MAD phasing (crystal grown at pH 7.5).

Resolution: 1.91→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed in remark 470 had little or no side chain density. Many residues at N-terminus had no or little visible density for protein backbone. The density for the ligand QUN ...Details: Residues listed in remark 470 had little or no side chain density. Many residues at N-terminus had no or little visible density for protein backbone. The density for the ligand QUN associated with chain B is not very good and is not included in the coordinates section. Some densities were modelled as water molecules even though the refined water molecules were greater than 3.5 Angstroms away from macromolecule atoms. These densities were indeed visible as discrete "water oxygen"-like densities but could represent moities other than water.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4412 -RANDOM
Rwork0.195 ---
all0.21 43822 --
obs0.199 43822 92.1 %-
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.98 Å20 Å2
2--0.61 Å20 Å2
3----1.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.91→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 87 377 4689
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.89
LS refinement shellResolution: 1.91→1.94 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.269 98 -
Rwork0.235 --
obs-946 39.1 %
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor all: 0.21 / Rfactor obs: 0.199 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Rfactor Rfree: 0.269 / Rfactor Rwork: 0.235

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