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

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Basic information

Entry
Database: PDB / ID: 5hij
TitleCrystal structure of glycine sarcosine N-methyltransferase from Methanohalophilus portucalensis in complex with betaine
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 / protein homotetramerization / methylation ...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 / protein homotetramerization / methylation / 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
TRIMETHYL GLYCINE / Class I SAM-dependent methyltransferase
Similarity search - Component
Biological speciesMethanohalophilus portucalensis FDF-1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _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)32,9182
Polymers32,8001
Non-polymers1181
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint4 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.176, 120.545, 131.368
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-434-

HOH

21A-464-

HOH

31A-471-

HOH

41A-505-

HOH

51A-557-

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-BET / TRIMETHYL GLYCINE


Mass: 118.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.15 Å3/Da / Density % sol: 60.94 %
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 and 1 mM 2-Mercaptoethanol. Crystallization reagent: 0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v ...Details: Protein solution: GSMT (6.6 mg/ml) in 100 mM TES pH 7.3, 2 M KCl, 1 mM EDTA and 1 mM 2-Mercaptoethanol. Crystallization reagent: 0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3,350. Betaine was soaked into crystals before data collection.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 27, 2015
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→20 Å / Num. obs: 31210 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rsym value: 0.054 / Net I/σ(I): 21.7
Reflection shellResolution: 1.93→2 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.3 / % 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 5HIL

5hil


Resolution: 1.93→19.724 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 1571 5.03 %Random selection
Rwork0.1658 ---
obs0.1678 31208 98.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→19.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 8 190 2160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072014
X-RAY DIFFRACTIONf_angle_d0.9642720
X-RAY DIFFRACTIONf_dihedral_angle_d12.785728
X-RAY DIFFRACTIONf_chiral_restr0.045283
X-RAY DIFFRACTIONf_plane_restr0.003356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9303-1.99260.26571410.21622389X-RAY DIFFRACTION90
1.9926-2.06370.23541370.19662690X-RAY DIFFRACTION100
2.0637-2.14620.24651400.18292697X-RAY DIFFRACTION100
2.1462-2.24380.18831380.17182692X-RAY DIFFRACTION100
2.2438-2.36190.23171440.17472708X-RAY DIFFRACTION100
2.3619-2.50960.21761460.18122710X-RAY DIFFRACTION100
2.5096-2.70290.2341430.19082703X-RAY DIFFRACTION100
2.7029-2.97410.28441460.18992722X-RAY DIFFRACTION100
2.9741-3.40260.22531450.16682725X-RAY DIFFRACTION100
3.4026-4.27960.1671420.13932761X-RAY DIFFRACTION100
4.2796-19.72520.1691490.14662840X-RAY DIFFRACTION98
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)
12.8905-1.0542-3.47632.31962.24557.1748-0.0970.2504-0.1172-0.17990.00420.12120.0625-0.47830.090.24360.0002-0.05620.1605-0.00640.2362-7.7312-16.3924-27.0515
22.33810.3867-0.24222.0153-1.14654.7496-0.0289-0.04730.0727-0.02080.03430.0819-0.20220.00820.00810.21490.0087-0.01860.1078-0.01860.1686-3.9222-7.1586-18.1376
32.5244-0.23760.03794.63953.71765.4516-0.0469-0.0607-0.18960.27120.06430.02010.24140.0937-0.00640.14940.00410.00110.21090.04340.137-3.6564-24.0323-13.4581
41.1854-0.13010.16841.3620.63722.5595-0.053-0.0254-0.16020.12170.05340.07340.2123-0.06960.00330.1855-0.00670.00820.18930.00360.2146-6.828-28.6372-21.0835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 263 )

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