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- PDB-3thr: Crystal structure of rat native liver Glycine N-methyltransferase... -

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Basic information

Entry
Database: PDB / ID: 3thr
TitleCrystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate monoglutamate
ComponentsGlycine N-methyltransferase
KeywordsTransferase/Transferase Inhibitor / Glycine N-methyltransferase / GNMT / Folate / methyltransferase / Folate Binding / Liver cytosol / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


selenol Se-methyltransferase activity / Glyoxylate metabolism and glycine degradation / glycine N-methyltransferase / glycine N-methyltransferase activity / sarcosine metabolic process / methyltransferase complex / methionine metabolic process / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process ...selenol Se-methyltransferase activity / Glyoxylate metabolism and glycine degradation / glycine N-methyltransferase / glycine N-methyltransferase activity / sarcosine metabolic process / methyltransferase complex / methionine metabolic process / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / folic acid binding / glycine binding / regulation of gluconeogenesis / glycogen metabolic process / one-carbon metabolic process / methylation / protein homotetramerization / identical protein binding / cytosol
Similarity search - Function
Glycine N-methyltransferase; chain A, domain 1 / Glycine N-methyltransferase, chain A, domain 1 / Glycine/Sarcosine N-methyltransferase / Glycine N-methyltransferase (EC 2.1.1.20 and EC 2.1.1.156) family profile. / Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich ...Glycine N-methyltransferase; chain A, domain 1 / Glycine N-methyltransferase, chain A, domain 1 / Glycine/Sarcosine N-methyltransferase / Glycine N-methyltransferase (EC 2.1.1.20 and EC 2.1.1.156) family profile. / Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / Glycine N-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLuka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Newcomer, M.E. / Wagner, C.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Differences in folate-protein interactions result in differing inhibition of native rat liver and recombinant glycine N-methyltransferase by 5-methyltetrahydrofolate.
Authors: Luka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Newcomer, M.E. / Wagner, C.
History
DepositionAug 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Sep 13, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: Glycine N-methyltransferase
B: Glycine N-methyltransferase
C: Glycine N-methyltransferase
D: Glycine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,27511
Polymers129,9474
Non-polymers2,3277
Water13,061725
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19150 Å2
ΔGint-63 kcal/mol
Surface area46220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.186, 83.788, 134.436
Angle α, β, γ (deg.)90.00, 91.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycine N-methyltransferase / Folate-binding protein


Mass: 32486.871 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P13255, glycine N-methyltransferase
#2: Chemical
ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H25N7O6
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M Na-fluoride or Ca-acetate, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 83512 / Num. obs: 83512 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.084 / Net I/σ(I): 22.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 7551 / Rsym value: 0.61 / % possible all: 84.5

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IDK

2idk


Resolution: 2→31.19 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.978 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24071 3723 4.8 %RANDOM
Rwork0.17812 ---
all0.18109 73600 --
obs0.18109 73600 87.1 %-
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: 14.829 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å20 Å2-1.23 Å2
2---1.52 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 2→31.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8984 0 165 725 9874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0229393
X-RAY DIFFRACTIONr_bond_other_d0.0010.026371
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.97212748
X-RAY DIFFRACTIONr_angle_other_deg1.069315437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78551139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23723.149416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.265151505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4981564
X-RAY DIFFRACTIONr_chiral_restr0.1250.21374
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021998
X-RAY DIFFRACTIONr_mcbond_it1.0611.55715
X-RAY DIFFRACTIONr_mcbond_other0.3061.52340
X-RAY DIFFRACTIONr_mcangle_it1.82129186
X-RAY DIFFRACTIONr_scbond_it2.87833674
X-RAY DIFFRACTIONr_scangle_it4.2824.53551
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 249 -
Rwork0.214 4411 -
obs-4411 71.31 %
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)
10.16020.0629-0.25540.35730.21210.79070.05130.09030.0165-0.0110.00680.1061-0.1182-0.2697-0.05810.23340.18280.0090.31150.08840.2485-2.324-2.24830.285
20.2637-0.19150.14060.7414-0.01711.94230.0313-0.01990.0225-0.13710.17430.0501-0.441-0.3929-0.20560.23840.1720.02080.27780.10130.1983-2.725-0.0511.681
30.0057-0.03890.0850.5357-0.63631.3058-0.01020.0045-0.0035-0.08440.009-0.0216-0.2231-0.00630.00110.23280.06810.00290.16990.00230.196726.699-20.70736.476
40.573-0.1975-0.03360.53270.24381.4661-0.02210.0307-0.0983-0.02360.00730.05840.09990.08720.01490.04680.05450.00650.08540.01880.124832.968-37.40335.415
51.0173-0.52450.85891.4333-0.37361.9362-0.0365-0.0999-0.04040.18080.14660.1268-0.2791-0.2279-0.11010.23840.21050.10810.20890.06690.1647-0.76212.72738.761
61.0209-0.03370.4511.86-0.37452.61120.00270.0422-0.053-0.23490.22650.12110.0492-0.3446-0.22920.08770.0149-0.05070.16820.0710.12320.893-15.6564.003
70.6826-0.3959-0.17391.39360.42641.24150.0337-0.01930.05890.1121-0.05740.0154-0.03930.00640.02370.03060.00590.00240.03310.00040.059225.429-22.11960.944
81.5908-0.55630.28510.82690.05611.63310.02740.1929-0.0927-0.2146-0.06140.11980.05570.08750.0340.09220.0401-0.02180.0935-0.00560.09429.969-36.54417.599
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 50
2X-RAY DIFFRACTION2B1 - 119
3X-RAY DIFFRACTION3C1 - 38
4X-RAY DIFFRACTION4D1 - 129
5X-RAY DIFFRACTION5A51 - 292
6X-RAY DIFFRACTION6B120 - 292
7X-RAY DIFFRACTION7C39 - 292
8X-RAY DIFFRACTION8D130 - 292

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