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- PDB-5lqc: Crystal Structure of COMT in complex with N-[(E)-3-[(2R,3S,4R,5R)... -

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Basic information

Entry
Database: PDB / ID: 5lqc
TitleCrystal Structure of COMT in complex with N-[(E)-3-[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-(methylamino)purin-9-yl]oxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide
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 / S-adenosylmethionine metabolic process / renin secretion into blood stream / dopamine secretion / catecholamine metabolic process / renal albumin absorption / artery development / habituation / cerebellar cortex morphogenesis / dopamine catabolic process / glomerulus development / response to salt / norepinephrine metabolic process / short-term memory / fear response / response to angiotensin / synaptic transmission, dopaminergic / cellular response to phosphate starvation / cellular response to cocaine / estrogen metabolic process / cholesterol efflux / response to food / prostaglandin metabolic process / negative regulation of dopamine metabolic process / response to pain / response to corticosterone / response to temperature stimulus / glycogen metabolic process / response to stress / startle response / exploration behavior / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / : / behavioral fear response / multicellular organismal response to stress / response to cytokine / response to amphetamine / female pregnancy / learning / negative regulation of smooth muscle cell proliferation / kidney development / visual learning / regulation of blood pressure / response to toxic substance / response to wounding / multicellular organism growth / response to estrogen / cognition / memory / cell body / response to lipopolysaccharide / methylation / vesicle / dendritic spine / response to oxidative stress / gene expression / postsynaptic membrane / response to hypoxia / learning or memory / 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-542 / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsEhler, A. / Ellermann, M. / Lerner, C. / Rudolph, M.G.
CitationJournal: To be published
Title: no title yet
Authors: Ellermann, M. / Lerner, C. / Rudolph, M.G.
History
DepositionAug 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)25,3333
Polymers24,7721
Non-polymers5612
Water99155
1
A: Catechol O-methyltransferase
hetero molecules

A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6666
Polymers49,5452
Non-polymers1,1224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4760 Å2
ΔGint-24 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.758, 50.758, 170.215
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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) / Gene: Comt / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22734, catechol O-methyltransferase
#2: Chemical ChemComp-542 / N-[(E)-3-[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-methylaminopurin-9-yl)oxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxy-benzamide


Mass: 536.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25FN6O6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: AMMONIUM SULPHATE, CHES, PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→56.74 Å / Num. obs: 20504 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 42.393 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.48
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.9-1.951.7020.820.315189.8
1.95-2.011.4421.220.552199.2
2.01-2.061.1851.810.679199.6
2.06-2.130.9612.350.816198.9
2.13-2.20.7333.150.863198.7
2.2-2.270.5673.990.968198.8
2.27-2.360.4515.180.955199.5
2.36-2.460.3656.420.969199.7
2.46-2.570.37.810.971199.8
2.57-2.690.239.710.984199.3
2.69-2.840.1812.20.988199
2.84-3.010.12915.910.994199.3
3.01-3.220.09919.470.993199.1
3.22-3.470.07423.870.996199.3
3.47-3.810.05927.880.998199.5
3.81-4.260.05330.810.998198.3
4.26-4.910.04233.920.998198
4.91-6.020.04533.460.998198.6
6.02-8.510.03633.970.999197.3
8.51-56.740.02735.810.999196.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.903→42.561 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.95
Details: domain-swapped structure, terminal beta strand is replaced by symmetry mate, but ligand binding unaffected
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 1011 4.94 %random
Rwork0.1994 ---
obs0.2018 20479 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.71 Å2 / Biso mean: 50.5259 Å2 / Biso min: 27.02 Å2
Refinement stepCycle: final / Resolution: 1.903→42.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 40 55 1772
Biso mean--42.56 44.14 -
Num. residues----213
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.58550.16961.25732.7083-0.46811.18570.2696-0.52970.36130.78830.04441.1113-0.204-0.9792-0.32761.065-0.04140.52370.38610.00390.76717.164722.070220.699
21.87440.96790.04911.8101-0.02592.12210.17430.00350.08920.7175-0.01570.3347-0.1432-0.1269-0.14460.6557-0.07450.15480.23390.01760.374228.760817.487611.3244
32.59480.7590.55262.64760.16490.15390.3638-0.3625-0.16941.2909-0.1511-0.0504-0.4654-0.0407-0.21091.0065-0.11480.07880.29350.00370.354633.164617.147118.1427
41.6498-0.5078-0.93351.373-0.37141.0584-0.2194-0.84970.56331.79820.0609-0.2620.0130.2546-0.20081.3829-0.13750.06870.3482-0.14850.203836.587824.299822.3781
52.9119-0.80080.06544.29380.21252.0765-0.2315-0.39030.11461.09190.2769-0.28-0.22110.0878-0.09880.667-0.0876-0.04510.2815-0.01020.381140.08121.285211.8665
66.5699-0.09151.46622.6572-0.6042.92240.04150.25140.0640.499-0.0255-0.0781-0.48680.494-0.08970.5165-0.1522-0.05050.25450.01560.332943.545727.34765.3412
71.67021.28320.15792.6182-0.44392.1094-0.02090.1706-0.02230.17390.1982-0.16630.02590.2269-0.18060.4121-0.0942-0.02220.2921-0.01950.334139.306719.30830.2427
83.4633-1.02550.27980.7459-0.95031.2294-0.3442-0.2378-0.17360.24220.3409-0.0835-0.15460.0230.02480.3821-0.09790.00330.3016-0.0480.43534.047834.22431.278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 35 )A4 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 70 )A36 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 92 )A71 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 130 )A93 - 130
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 143 )A131 - 143
6X-RAY DIFFRACTION6chain 'A' and (resid 144 through 156 )A144 - 156
7X-RAY DIFFRACTION7chain 'A' and (resid 157 through 195 )A157 - 195
8X-RAY DIFFRACTION8chain 'A' and (resid 196 through 216 )A196 - 216

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