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

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Basic information

Entry
Database: PDB / ID: 3ths
TitleCrystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate pentaglutamate
Components
  • 5-methyltetrahydrofolate pentaglutamate
  • Glycine N-methyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Glycine N-methyltransferase / GNMT / Folate / Folate binding / Transferase / 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 / regulation of gluconeogenesis / glycine binding / 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-methyltetrahydrofolate pentaglutamate / BETA-MERCAPTOETHANOL / Glycine N-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Dec 12, 2012Group: Other
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_polymer_linkage / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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
E: 5-methyltetrahydrofolate pentaglutamate
F: 5-methyltetrahydrofolate pentaglutamate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,1418
Polymers131,8996
Non-polymers2412
Water1,58588
1
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)130,1896
Polymers129,9474
Non-polymers2412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14950 Å2
ΔGint-59 kcal/mol
Surface area47480 Å2
MethodPISA
2
E: 5-methyltetrahydrofolate pentaglutamate


  • defined by author&software
  • 976 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)9761
Polymers9761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
F: 5-methyltetrahydrofolate pentaglutamate


  • defined by author&software
  • 976 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)9761
Polymers9761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)193.036, 61.047, 146.352
Angle α, β, γ (deg.)90.00, 128.92, 90.00
Int Tables number5
Space group name H-MC121

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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: Protein/peptide 5-methyltetrahydrofolate pentaglutamate


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 975.911 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: 5-methyltetrahydrofolate pentaglutamate
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
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: 2.5→48.22 Å / Num. all: 46441 / Num. obs: 46441 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 62.4 Å2 / Rsym value: 0.081 / Net I/σ(I): 34.1
Reflection shellResolution: 2.5→2.565 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3 / Num. unique all: 4533 / Rsym value: 0.565 / % possible all: 98.5

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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: 2.5→48.22 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 26.305 / SU ML: 0.267 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27981 2250 4.9 %RANDOM
Rwork0.22781 ---
all0.23035 43978 --
obs0.23035 43978 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.955 Å2
Baniso -1Baniso -2Baniso -3
1--4.45 Å20 Å2-0.8 Å2
2--4.35 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8984 0 15 88 9087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229224
X-RAY DIFFRACTIONr_bond_other_d0.0020.026239
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.96212513
X-RAY DIFFRACTIONr_angle_other_deg0.938315111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9951127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67523.114411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.576151483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4671564
X-RAY DIFFRACTIONr_chiral_restr0.0850.21357
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110269
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021955
X-RAY DIFFRACTIONr_mcbond_it0.6341.55654
X-RAY DIFFRACTIONr_mcbond_other0.1421.52325
X-RAY DIFFRACTIONr_mcangle_it1.23629073
X-RAY DIFFRACTIONr_scbond_it1.92733566
X-RAY DIFFRACTIONr_scangle_it3.1464.53432
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 172 -
Rwork0.278 3194 -
obs-3194 98.13 %
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)
13.10240.4326-0.69970.42550.04870.93250.0288-0.4863-0.3603-0.0051-0.03630.06870.08130.03830.00750.0774-0.0582-0.03090.12060.06620.1982-51.122517.472726.0143
24.95130.54210.39992.17480.37041.5089-0.0373-0.9189-0.06710.2811-0.0320.21460.072-0.02110.06930.1028-0.10850.03920.45340.04960.0906-53.128622.617239.9959
31.97120.0173-0.70410.8060.79621.77120.0742-0.0478-0.31720.0026-0.14330.09360.2251-0.03650.06910.15710.0136-0.07720.0413-0.00470.1923-31.396911.22196.9985
43.4035-0.4754-0.31533.63461.5862.27760.10810.2745-0.0599-0.29760.0307-0.1905-0.04640.1395-0.13890.1335-0.0105-0.03910.04130.00750.0982-19.852217.0780.2352
51.3923-0.0352-0.85321.1448-0.07322.80750.1802-1.00060.47930.27780.00710.0872-0.46080.2864-0.18730.2303-0.15830.05680.8433-0.31930.2864-16.322645.93251.7045
64.86141.2749-0.13052.85870.58955.51780.1257-1.30710.60590.34910.22690.2903-0.48010.0322-0.35260.1304-0.05340.10890.9066-0.25430.2522-29.99643.497156.4953
74.63091.251-1.05680.6694-0.16261.49430.2171-0.57040.38950.0748-0.23190.0846-0.03080.08770.01480.0839-0.069-0.01190.146-0.08860.2011-0.936147.394227.9752
85.57272.7665-0.43462.91310.4442.67410.1194-0.02120.0382-0.0144-0.0007-0.18210.13240.3951-0.11870.08450.0119-0.02160.1528-0.0940.1472.47639.903915.6445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 190
2X-RAY DIFFRACTION2A191 - 292
3X-RAY DIFFRACTION3B1 - 190
4X-RAY DIFFRACTION4B191 - 292
5X-RAY DIFFRACTION5C1 - 191
6X-RAY DIFFRACTION6C192 - 292
7X-RAY DIFFRACTION7D1 - 190
8X-RAY DIFFRACTION8D191 - 292

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