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- PDB-3a7e: Crystal structure of human COMT complexed with SAM and 3,5-dinitr... -

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Basic information

Entry
Database: PDB / ID: 3a7e
TitleCrystal structure of human COMT complexed with SAM and 3,5-dinitrocatechol
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / COMT / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / MAGNESIUM / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / S-ADENOSYL-L-METHIONINE / Cell membrane / Membrane / Metal-binding / Phosphoprotein / Signal-anchor / Transmembrane
Function / homology
Function and homology information


Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / renal sodium excretion / : / : ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / renal sodium excretion / : / : / catechol O-methyltransferase / renal filtration / developmental process / renin secretion into blood stream / dopamine secretion / Methylation / renal albumin absorption / habituation / artery development / response to salt / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / cellular response to phosphate starvation / glomerulus development / synaptic transmission, dopaminergic / O-methyltransferase activity / response to angiotensin / cellular response to cocaine / exploration behavior / response to food / cholesterol efflux / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / dopamine metabolic process / startle response / detection of temperature stimulus involved in sensory perception of pain / : / behavioral fear response / response to amphetamine / methyltransferase activity / response to cytokine / visual learning / multicellular organism growth / response to toxic substance / memory / response to wounding / gene expression / methylation / response to oxidative stress / Potential therapeutics for SARS / response to hypoxia / response to xenobiotic stimulus / axon / intracellular membrane-bounded organelle / synapse / dendrite / magnesium ion binding / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Catechol O-methyltransferase, eukaryotic / O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,5-DINITROCATECHOL / S-ADENOSYLMETHIONINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTsuji, E.
CitationJournal: To be Published
Title: Hit to Lead: Comprehensive Strategy of de novo Scaffold Generation by FBDD. Part 1: In silico Fragments Linking and Verification of Spatial Proximity using Inter Ligand NOE Approachs
Authors: Nonaka, Y. / Momose, T. / Ozawa, T. / Ozawa, M. / Nakatsu, M. / Tsuji, E. / Okazaki, K. / Takase, Y. / Kiyotani, T.
History
DepositionSep 26, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6494
Polymers24,0271
Non-polymers6233
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.909, 50.909, 168.186
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Catechol O-methyltransferase


Mass: 24026.602 Da / Num. of mol.: 1 / Fragment: UNP residues 51-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMT / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON PLUS (DE3) RP / References: UniProt: P21964, catechol O-methyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-DNC / 3,5-DINITROCATECHOL


Mass: 200.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N2O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON ISOFORM SOLUBLE OF P21964(COMT_HUMAN).

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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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes pH7.5, 2% (v/v) PEG 400, 2.0M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1.5418 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 21, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→28 Å / Num. all: 6717 / Num. obs: 6727 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.163 / Rsym value: 0.137 / Net I/σ(I): 4.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 12.7 / Num. unique all: 955 / Rsym value: 0.352 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BSSat BL32B2data collection
AMoREphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VID

1vid


Resolution: 2.8→10 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.821 / SU B: 17.41 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29819 654 10 %RANDOM
Rwork0.21769 ---
obs0.22558 5888 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å20 Å2
2--0.19 Å20 Å2
3----0.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.471 Å0.378 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1660 0 42 46 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221733
X-RAY DIFFRACTIONr_angle_refined_deg0.9122.0012352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4755211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61824.86876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.17115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.248159
X-RAY DIFFRACTIONr_chiral_restr0.0670.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211297
X-RAY DIFFRACTIONr_mcbond_it0.6041.51059
X-RAY DIFFRACTIONr_mcangle_it1.19521707
X-RAY DIFFRACTIONr_scbond_it1.913674
X-RAY DIFFRACTIONr_scangle_it3.1844.5645
LS refinement shellResolution: 2.8→2.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 46 -
Rwork0.199 394 -
obs--100 %

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