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- PDB-4pyo: Humanized rat COMT bound to SAH, semi-holo form -

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Basic information

Entry
Database: PDB / ID: 4pyo
TitleHumanized rat COMT bound to SAH, semi-holo form
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / CELL MEMBRANE / MEMBRANE / METAL-BINDING / PHOSPHOPROTEIN / SIGNAL-ANCHOR / TRANSMEMBRANE ANCHOR / ENZYME MECHANISM / CONFORMATIONAL CHANGE
Function / homology
Function and homology information


: / response to olanzapine / response to risperidone / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process ...: / response to olanzapine / response to risperidone / 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 / renal sodium excretion / developmental process / renal filtration / S-adenosylmethionine metabolic process / renin secretion into blood stream / catecholamine metabolic process / dopamine secretion / renal albumin absorption / habituation / artery development / cerebellar cortex morphogenesis / dopamine catabolic process / response to salt / glomerulus development / norepinephrine metabolic process / response to angiotensin / fear response / short-term memory / synaptic transmission, dopaminergic / cellular response to phosphate starvation / cellular response to cocaine / estrogen metabolic process / cholesterol efflux / prostaglandin metabolic process / response to pain / response to food / response to corticosterone / response to temperature stimulus / glycogen metabolic process / negative regulation of dopamine metabolic process / startle response / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / exploration behavior / response to stress / multicellular organismal response to stress / behavioral fear response / response to cytokine / response to amphetamine / learning / kidney development / negative regulation of smooth muscle cell proliferation / female pregnancy / visual learning / response to wounding / response to toxic substance / response to estrogen / regulation of blood pressure / cognition / multicellular organism growth / memory / cell body / response to oxidative stress / response to lipopolysaccharide / methylation / vesicle / gene expression / dendritic spine / postsynaptic membrane / 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
: / S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEhler, A. / Benz, J. / Schlatter, D. / Rudolph, M.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Mapping the conformational space accessible to catechol-O-methyltransferase.
Authors: Ehler, A. / Benz, J. / Schlatter, D. / Rudolph, M.G.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

Downloads & links

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Assembly

Deposited unit
A: Catechol O-methyltransferase
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2216
Polymers49,3892
Non-polymers8324
Water1,928107
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1183
Polymers24,6941
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1033
Polymers24,6941
Non-polymers4092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.369, 60.380, 148.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Catechol O-methyltransferase


Mass: 24694.332 Da / Num. of mol.: 2 / Mutation: M134I, Y138C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli (E. coli) / References: UniProt: P22734, catechol O-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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 293 K / Details: VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45.9 Å / Num. obs: 31280 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.11322 / Net I/σ(I): 10.2398
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.5045 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1448)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.88 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 29.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 1572 5.03 %
Rwork0.189 --
obs0.191 31244 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 54 107 3523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073480
X-RAY DIFFRACTIONf_angle_d1.0584721
X-RAY DIFFRACTIONf_dihedral_angle_d15.071317
X-RAY DIFFRACTIONf_chiral_restr0.044536
X-RAY DIFFRACTIONf_plane_restr0.004601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.38551380.33062637X-RAY DIFFRACTION100
2.1678-2.24530.36741440.28942661X-RAY DIFFRACTION99
2.2453-2.33520.2941360.28692615X-RAY DIFFRACTION98
2.3352-2.44140.30591450.24342651X-RAY DIFFRACTION100
2.4414-2.57010.28461430.22372666X-RAY DIFFRACTION100
2.5701-2.73110.26991480.22452677X-RAY DIFFRACTION100
2.7311-2.9420.26791340.2222695X-RAY DIFFRACTION100
2.942-3.2380.24931280.2022725X-RAY DIFFRACTION100
3.238-3.70630.23711450.17322710X-RAY DIFFRACTION99
3.7063-4.66890.17751530.14062750X-RAY DIFFRACTION100
4.6689-45.88860.18631580.15462885X-RAY DIFFRACTION100
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)
17.37570.6943-2.32479.48030.98056.66830.0581-0.00331.1197-0.40.5576-0.913-1.07941.1207-0.52630.5262-0.20770.06650.6456-0.12240.763423.2789.3702-30.6377
26.102-1.09381.43375.07851.14682.59920.14760.43140.4611-0.71530.0193-0.59670.43410.6854-0.19090.5992-0.04160.05760.4349-0.04890.33128.59045.6511-23.8306
33.29670.98610.39442.92051.29544.7054-0.0889-0.1931-0.14510.48160.1701-0.48440.64450.5341-0.06370.3730.0874-0.06990.2978-0.00270.351514.347-7.9654-29.9196
41.7486-1.0803-0.02524.36380.47654.39380.0246-0.0169-0.14710.2951-0.12750.15830.2443-0.07780.09630.3526-0.02950.02810.2272-0.0150.2438-2.2745-3.2063-28.7118
53.1201-0.9372-1.34344.0328-4.93358.18290.27210.1107-0.7364-0.2508-0.54880.25370.7248-0.16970.07430.4388-0.0392-0.01910.4546-0.00420.4009-13.440718.2734-21.5066
68.16674.2535-4.98482.669-3.98348.93080.3031-0.27781.03890.3220.16790.7386-0.9878-0.6257-0.48130.56570.07830.04440.3757-0.00840.421-11.956929.2475-18.6065
78.48023.1313.88013.88352.13384.3473-0.0471-1.17090.32210.6407-0.2303-0.0651-0.17-0.88790.35920.9240.06750.0830.6623-0.09530.5414-5.336929.6259-7.3959
85.0537-0.80132.50612.01780.68744.36510.0120.01830.25090.04540.023-0.1583-0.19070.2771-0.03150.5392-0.04380.05260.3212-0.00080.28755.037422.2764-15.6161
96.9876-0.23461.50254.1487-0.43676.01810.0202-0.70510.0280.40110.0468-0.26450.27440.07-0.08540.5201-0.0065-0.07990.3897-0.07620.2789.09419.4643-3.2725
103.5061-1.1641-1.35131.6587-0.46571.9734-0.2902-1.0030.35260.82370.2136-0.3064-0.46150.11410.07090.8442-0.0426-0.10730.7042-0.15820.39214.365425.18124.0054
116.6820.6763-1.61522.284-0.39731.0525-0.4583-0.72290.80320.61190.3994-0.0091-0.0630.1025-0.00921.03480.0132-0.07020.6688-0.07580.3981-1.086626.25752.5527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 46:79 )A46 - 79
2X-RAY DIFFRACTION2( CHAIN A AND RESID 80:100 )A80 - 100
3X-RAY DIFFRACTION3( CHAIN A AND RESID 101:186 )A101 - 186
4X-RAY DIFFRACTION4( CHAIN A AND RESID 187:259 )A187 - 259
5X-RAY DIFFRACTION5( CHAIN B AND RESID 45:59 )B45 - 59
6X-RAY DIFFRACTION6( CHAIN B AND RESID 60:78 )B60 - 78
7X-RAY DIFFRACTION7( CHAIN B AND RESID 79:100 )B79 - 100
8X-RAY DIFFRACTION8( CHAIN B AND RESID 101:173 )B101 - 173
9X-RAY DIFFRACTION9( CHAIN B AND RESID 174:199 )B174 - 199
10X-RAY DIFFRACTION10( CHAIN B AND RESID 200:232 )B200 - 232
11X-RAY DIFFRACTION11( CHAIN B AND RESID 242:259 )B242 - 259

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