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- PDB-1h1d: Catechol O-Methyltransferase -

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Basic information

Entry
Database: PDB / ID: 1h1d
TitleCatechol O-Methyltransferase
ComponentsCATECHOL-O-METHYLTRANSFERASE
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION
Function / homology
Function and homology information


positive regulation of homocysteine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process ...positive regulation of homocysteine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / developmental process / renal sodium excretion / renal filtration / negative regulation of dopamine metabolic process / S-adenosylmethionine metabolic process / renin secretion into blood stream / dopamine secretion / catecholamine metabolic process / renal albumin absorption / habituation / artery development / short-term memory / cerebellar cortex morphogenesis / response to salt / dopamine catabolic process / glomerulus development / norepinephrine metabolic process / fear response / synaptic transmission, dopaminergic / cellular response to phosphate starvation / response to angiotensin / cellular response to cocaine / estrogen metabolic process / exploration behavior / cholesterol efflux / response to food / prostaglandin metabolic process / response to corticosterone / response to temperature stimulus / response to pain / glycogen metabolic process / response to stress / startle response / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / behavioral fear response / multicellular organismal response to stress / response to amphetamine / response to cytokine / learning / kidney development / female pregnancy / negative regulation of smooth muscle cell proliferation / visual learning / multicellular organism growth / : / regulation of blood pressure / response to wounding / memory / cognition / response to toxic substance / response to estrogen / cell body / gene expression / methylation / vesicle / response to lipopolysaccharide / postsynaptic membrane / dendritic spine / response to oxidative stress / learning or memory / response to hypoxia / postsynapse / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / magnesium ion binding / membrane / cytosol
Similarity search - Function
Catechol O-methyltransferase, eukaryotic / Class I-like SAM-dependent O-methyltransferase / 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
Chem-BIA / S-ADENOSYLMETHIONINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsArcher, M. / Rodrigues, M.L. / Matias, P.M. / Bonifacio, M.J. / Learmonth, D.A. / Soares-da-Silva, P. / Carrondo, M.A.
Citation
Journal: Mol.Pharmacol. / Year: 2002
Title: Kinetics and Crystal Structure of Catechol-O-Methyltransferase Complex with Co-Substrate and a Novel Inhibitor with Potential Therapeutic Application
Authors: Bonifacio, M.J. / Archer, M. / Rodrigues, M.L. / Matias, P.M. / Learmonth, D.A. / Carrondo, M.A. / Soares-da-Silva, P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary Crystallographic Characterization of Catechol-O-Methyltransferase in Complex with its Co-Substrate and an Inhibitor
Authors: Rodrigues, M.L. / Archer, M. / Bonifacio, M.J. / Soares-da-Silva, P. / Carrondo, M.A.
History
DepositionJul 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2003Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2May 30, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / struct
Item: _audit_author.name / _citation_author.name / _struct.title
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: CATECHOL-O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6354
Polymers24,7721
Non-polymers8623
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.490, 51.490, 168.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2086-

HOH

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Components

#1: Protein CATECHOL-O-METHYLTRANSFERASE


Mass: 24772.400 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 44-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Tissue: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: P22734, 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-BIA / 1-(3,4,DIHYDROXY-5-NITROPHENYL)-3-{4-[3-(TRIFLUOROMETHYL) PHENYL] PIPERAZIN-1-YL}PROPAN-1-ONE / BIA 3-335


Mass: 439.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20F3N3O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: CATALYZES THE INACTIVATION, OF CATECHOLAMINE NEUROTRANSMITTERS AND CATECHOL VIA O- ...FUNCTION: CATALYZES THE INACTIVATION, OF CATECHOLAMINE NEUROTRANSMITTERS AND CATECHOL VIA O-METHYLATION. ISOFORM: SOLUBLE ISOFORM COMPRISES RESIDUES 44-264 OF THE MEMBRANE BOUND FORM (RESIDUES 1-264) OF THE PROTEIN.

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 5.5 / Details: 8-10% PEG 6K, 0.1 M MES PH 5.5 - 6.5
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: Rodrigues, M.L., (2001) Acta Crystallogr.,Sect.D, D57, 906.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.5 M1dropNaCl
28-10 %PEG60001reservoir
30.1 MMES1reservoirpH5.5-6.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25.7 Å / Num. obs: 131542 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.2
Reflection shellResolution: 2.02→2.09 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.2 / % possible all: 95.3
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 21.4 Å / Num. obs: 17663 / Redundancy: 7.4 % / Num. measured all: 131542 / Rmerge(I) obs: 0.113
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VID

1vid


Resolution: 2→25.8 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.198 889 5 %RANDOM
Rwork0.174 ---
obs0.174 17627 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å22.04 Å20 Å2
2--2.52 Å20 Å2
3----5.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 59 93 1832
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.322.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 127 5.3 %
Rwork0.278 2259 -
obs--79.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WAT_REP.PARSAM.TOP
X-RAY DIFFRACTION3ION.PARBIA.TOP
X-RAY DIFFRACTION4LIGAND.PAR
Refinement
*PLUS
Lowest resolution: 21.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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