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- PDB-6lfe: Rat-COMT, Nitecapone,SAM and Mg bond -

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Basic information

Entry
Database: PDB / ID: 6lfe
TitleRat-COMT, Nitecapone,SAM and Mg bond
ComponentsCatechol O-methyltransferaseCatechol-O-methyltransferase
KeywordsTRANSFERASE / Enzyme S-adenosylmethionone catechol / catecholamine
Function / homology
Function and homology information


Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol-containing compound metabolic process / S-adenosylhomocysteine metabolic process ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol-containing compound metabolic process / S-adenosylhomocysteine metabolic process / response to salt / catechol O-methyltransferase activity / renal sodium excretion / : / : / renin secretion into blood stream / catechol O-methyltransferase / developmental process / renal filtration / renal albumin absorption / dopamine secretion / S-adenosylmethionine metabolic process / negative regulation of dopamine metabolic process / habituation / artery development / catecholamine metabolic process / short-term memory / cellular response to phosphate starvation / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / glomerulus development / fear response / multicellular organismal reproductive process / synaptic transmission, dopaminergic / response to angiotensin / cellular response to cocaine / estrogen metabolic process / response to food / exploration behavior / cholesterol efflux / response to temperature stimulus / response to pain / dopamine metabolic process / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / startle response / detection of temperature stimulus involved in sensory perception of pain / response to inorganic substance / behavioral fear response / multicellular organismal response to stress / response to amphetamine / response to organic substance / kidney development / learning / female pregnancy / response to cytokine / negative regulation of smooth muscle cell proliferation / multicellular organism growth / visual learning / response to organic cyclic compound / memory / response to toxic substance / cognition / regulation of blood pressure / response to wounding / response to estrogen / cell body / gene expression / methylation / postsynapse / postsynaptic membrane / response to oxidative stress / vesicle / response to lipopolysaccharide / dendritic spine / response to hypoxia / learning or memory / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / magnesium ion binding / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-EAO / ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsTakebe, K. / Iijima, H. / Suzuki, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP15K08034 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101001 (0318) Japan
CitationJournal: Chem Pharm Bull (Tokyo) / Year: 2020
Title: Crystal Structure of Catechol O-Methyltransferase Complexed with Nitecapone.
Authors: Iijima, H. / Takebe, K. / Suzuki, M. / Kobayashi, H. / Takamiya, T. / Saito, H. / Niwa, N. / Kuwada-Kusunose, T.
History
DepositionDec 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 9, 2022Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)25,9378
Polymers24,9171
Non-polymers1,0207
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint9 kcal/mol
Surface area9100 Å2
Unit cell
Length a, b, c (Å)49.665, 53.298, 80.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catechol O-methyltransferase / Catechol-O-methyltransferase


Mass: 24916.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22734, catechol O-methyltransferase

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Non-polymers , 6 types, 234 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EAO / 3-(3,4-dihydroxy-5-nitrobenzylidene)pentane-2,4-dione / Nitecapone


Mass: 265.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11NO6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES sodium pH 7.5 10%v/v 2-propanol 20%w/v polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→49.67 Å / Num. obs: 28732 / % possible obs: 99.2 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Net I/σ(I): 13.7
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 1262 / CC1/2: 0.907

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VID

1vid


Resolution: 1.6→9.922 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1661 1431 5.02 %
Rwork0.1469 27087 -
obs0.1478 28518 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.79 Å2 / Biso mean: 19.8929 Å2 / Biso min: 8.14 Å2
Refinement stepCycle: final / Resolution: 1.6→9.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 69 230 1972
Biso mean--23.36 34.55 -
Num. residues----213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.65690.22711400.18682506264693
1.6569-1.7230.2211360.16622649278598
1.723-1.80090.18881450.15626622807100
1.8009-1.89530.18061600.148927012861100
1.8953-2.01310.15911580.146326892847100
2.0131-2.1670.16461500.142227112861100
2.167-2.38230.18551320.14327362868100
2.3823-2.72080.17411190.146927712890100
2.7208-3.40480.15661800.151727432923100
3.4048-9.92190.14081110.138229193030100
Refinement TLS params.Method: refined / Origin x: 20.8071 Å / Origin y: -4.4962 Å / Origin z: -9.1019 Å
111213212223313233
T0.1073 Å20.0073 Å20.0071 Å2-0.0932 Å20.0066 Å2--0.1174 Å2
L0.9643 °2-0.1933 °20.1944 °2-0.3543 °2-0.1198 °2--0.8528 °2
S-0.0057 Å °0.0719 Å °0.1123 Å °0.0056 Å °-0.0418 Å °-0.0325 Å °-0.0106 Å °0.0009 Å °-0.096 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 215
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allS1 - 234
6X-RAY DIFFRACTION1allS238 - 244
7X-RAY DIFFRACTION1allS245 - 246
8X-RAY DIFFRACTION1allS247 - 249
9X-RAY DIFFRACTION1allS250 - 251
10X-RAY DIFFRACTION1allS252
11X-RAY DIFFRACTION1allE1 - 3
12X-RAY DIFFRACTION1allF1
13X-RAY DIFFRACTION1allF3

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