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- PDB-5him: Crystal structure of glycine sarcosine N-methyltransferase from M... -

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Basic information

Entry
Database: PDB / ID: 5him
TitleCrystal structure of glycine sarcosine N-methyltransferase from Methanohalophilus portucalensis in complex with S-adenosylhomocysteine and dimethylglycine
ComponentsGlycine sarcosine N-methyltransferase
KeywordsTRANSFERASE / S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase) / class I / monomethylation of glycine and sarcosine / rate-limiting enzyme in betaine biosynthesis / betaine-mediated feedback inhibition
Function / homology
Function and homology information


sarcosine metabolic process / glycine N-methyltransferase activity / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / regulation of gluconeogenesis / glycine binding / one-carbon metabolic process / methylation / protein homotetramerization ...sarcosine metabolic process / glycine N-methyltransferase activity / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / regulation of gluconeogenesis / glycine binding / one-carbon metabolic process / methylation / protein homotetramerization / identical protein binding / cytosol
Similarity search - Function
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N,N-DIMETHYLGLYCINE / S-ADENOSYL-L-HOMOCYSTEINE / Class I SAM-dependent methyltransferase
Similarity search - Component
Biological speciesMethanohalophilus portucalensis FDF-1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.338 Å
AuthorsLee, Y.R. / Lin, T.S. / Lai, S.J. / Liu, M.S. / Lai, M.C. / Chan, N.L.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Ministry of Science and TechnologyNSC101-2911-I-002-303, 103-2113-M-002-010-MY3, 104-2911-I-002-302 Taiwan
National Taiwan University104R7614-3 and 104R7560-4 Taiwan
Ministry of Education, Taiwan ROC, under the ATU plan to NLCNational Chung Hsing University Taiwan
CitationJournal: Sci Rep / Year: 2016
Title: Structural Analysis of Glycine Sarcosine N-methyltransferase from Methanohalophilus portucalensis Reveals Mechanistic Insights into the Regulation of Methyltransferase Activity
Authors: Lee, Y.R. / Lin, T.S. / Lai, S.J. / Liu, M.S. / Lai, M.C. / Chan, N.L.
History
DepositionJan 12, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Nov 8, 2023Group: 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine sarcosine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6609
Polymers32,8001
Non-polymers8608
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint20 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.975, 121.219, 131.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-418-

HOH

31A-429-

HOH

41A-431-

HOH

51A-475-

HOH

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Components

#1: Protein Glycine sarcosine N-methyltransferase


Mass: 32800.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanohalophilus portucalensis FDF-1 (archaea)
Strain: FDF-1 / Gene: gsmt / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6KV61, EC: 2.1.1.156
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-DMG / N,N-DIMETHYLGLYCINE / DIMETHYLGLYCINE


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: Protein solution: GSMT (6.6 mg/ml) in 100 mM TES pH 7.3, 2 M KCl, 1 mM EDTA, 1 mM 2-Mercaptoethanol, 0.1 mM SAH and 0.2 M betaine. Crystallization reagent: 0.1 M Tris-HCl pH 8.5 and 1.5 M ...Details: Protein solution: GSMT (6.6 mg/ml) in 100 mM TES pH 7.3, 2 M KCl, 1 mM EDTA, 1 mM 2-Mercaptoethanol, 0.1 mM SAH and 0.2 M betaine. Crystallization reagent: 0.1 M Tris-HCl pH 8.5 and 1.5 M sodium chloride. SAH and dimethylglycine were soaked into crystals before data collection.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 19, 2012
RadiationMonochromator: Horizontally Focusing Single Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.338→30 Å / Num. obs: 17982 / % possible obs: 100 % / Redundancy: 5.9 % / Rsym value: 0.078 / Net I/σ(I): 20.6
Reflection shellResolution: 2.338→2.42 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedata collection
HKL-2000data scaling
HKL-2000data processing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XVA

1xva


Resolution: 2.338→27.529 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.207 891 4.96 %Random selection
Rwork0.156 ---
obs0.1586 17980 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.338→27.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 57 78 2090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082061
X-RAY DIFFRACTIONf_angle_d1.0012775
X-RAY DIFFRACTIONf_dihedral_angle_d14.566734
X-RAY DIFFRACTIONf_chiral_restr0.039290
X-RAY DIFFRACTIONf_plane_restr0.004359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3377-2.48410.25111400.19852745X-RAY DIFFRACTION98
2.4841-2.67570.24161550.19022806X-RAY DIFFRACTION100
2.6757-2.94470.22921420.19242829X-RAY DIFFRACTION100
2.9447-3.37010.2121440.17452847X-RAY DIFFRACTION100
3.3701-4.24350.18221500.13642875X-RAY DIFFRACTION100
4.2435-27.53080.19881600.13472987X-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)
14.0284-1.831-3.27134.46263.25378.0076-0.03260.1322-0.3046-0.2429-0.05360.416-0.1912-0.39080.10120.27720.009-0.04210.20080.0070.3523-7.7981-14.6701-24.6264
27.2951-0.7735-0.26856.2649-1.33644.1597-0.2094-0.0024-0.01760.03540.14120.0946-0.2475-0.04160.05880.27730.0043-0.02790.1422-0.01590.2121-3.4174-6.908-20.5437
34.6221-0.90210.16367.29061.38884.8445-0.1817-0.32010.11910.82650.2621-0.0409-0.06520.2615-0.07440.33220.04690.01340.31090.00810.1908-2.7979-17.3001-10.056
40.87280.3435-0.66333.36780.70942.8409-0.02440.2443-0.2475-0.08540.08580.17080.3919-0.0924-0.07270.22720.00920.00040.3878-0.04490.341-3.2709-31.6674-28.2514
56.09951.08133.30754.11012.19186.5101-0.231-0.7112-0.37021.32220.26290.84430.5174-0.4768-0.13950.70660.09650.17030.35280.12920.3576-8.8607-26.8309-6.5754
64.07163.30095.75285.99725.52359.42880.3021-0.139-0.2270.6447-0.38310.48950.6007-0.8183-0.15910.2681-0.01980.08460.29870.02290.3931-14.3236-27.5309-18.9994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 167 )
4X-RAY DIFFRACTION4chain 'A' and (resid 168 through 222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 243 )
6X-RAY DIFFRACTION6chain 'A' and (resid 244 through 263 )

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