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

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Basic information

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


glycine N-methyltransferase activity / sarcosine metabolic process / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / glycine binding / regulation of gluconeogenesis / one-carbon metabolic process / methylation / protein homotetramerization ...glycine N-methyltransferase activity / sarcosine metabolic process / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / glycine binding / regulation of gluconeogenesis / 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
S-ADENOSYLMETHIONINE / SARCOSINE / Class I SAM-dependent methyltransferase
Similarity search - Component
Biological speciesMethanohalophilus portucalensis FDF-1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.205 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
DepositionSep 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references / Experimental preparation
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

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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)33,5367
Polymers32,8001
Non-polymers7366
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.733, 120.710, 130.922
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-430-

HOH

21A-440-

HOH

31A-452-

HOH

41A-489-

HOH

51A-497-

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)
Gene: gsmt / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6KV61
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-SAR / SARCOSINE / Sarcosine


Type: peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.12 Å3/Da / Density % sol: 65.23 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.3
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 sarcosine. Crystallization reagent: 0.2 M Potassium sodium tartrate ...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 sarcosine. Crystallization reagent: 0.2 M Potassium sodium tartrate tetrahydrate and 20% (w/v) Polyethylene Glycol 3350. 2 mM SAM and 685 mM sarcosine 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 315r / Detector: CCD / Date: Aug 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.205→29.195 Å / Num. obs: 20701 / % possible obs: 97.98 % / Redundancy: 3.5 % / Net I/σ(I): 18.075
Reflection shellResolution: 2.2→2.28 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Blu-Icedata collection
HKL-2000data scaling
HKL-2000data processing
PHENIX1.10.1_2155model building
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HIL

5hil


Resolution: 2.205→29.195 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 1039 5.02 %
Rwork0.1734 --
obs0.175 20698 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.205→29.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 49 97 2130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072078
X-RAY DIFFRACTIONf_angle_d0.8152804
X-RAY DIFFRACTIONf_dihedral_angle_d12.0911198
X-RAY DIFFRACTIONf_chiral_restr0.05295
X-RAY DIFFRACTIONf_plane_restr0.004364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.205-2.32120.24751320.20922699X-RAY DIFFRACTION96
2.3212-2.46660.25721620.19732786X-RAY DIFFRACTION99
2.4666-2.65690.23251400.19112787X-RAY DIFFRACTION99
2.6569-2.92410.23531490.1882799X-RAY DIFFRACTION99
2.9241-3.34670.20411470.17122819X-RAY DIFFRACTION99
3.3467-4.21440.1681520.15662850X-RAY DIFFRACTION98
4.2144-29.19740.19831570.16732919X-RAY DIFFRACTION97
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)
12.8496-1.54073.6157.0120.00136.391-0.23610.15760.85890.04120.4149-1.0089-0.18910.719-0.06360.3779-0.00240.01780.41-0.14560.42765.5439-17.9462-31.5789
29.5951-1.315-6.27451.86620.53674.77130.00720.3066-0.5966-0.2367-0.01970.49540.3933-1.04020.02430.2854-0.0366-0.07570.36-0.02620.5777-17.5299-14.3202-22.0901
34.27630.7114-1.20113.1836-1.45283.8201-0.1438-0.10670.0372-0.05580.04110.1247-0.03930.0490.08090.2807-0.0019-0.00090.2225-0.0220.2559-4.1061-7.2086-18.0521
43.8104-1.24880.43767.86942.89794.5929-0.1037-0.1516-0.030.33760.0758-0.03950.14440.14570.03220.2525-0.01290.03040.30320.03140.2145-2.9897-20.122-10.711
59.1577-3.28537.36435.4064-3.0568.83460.39010.1616-0.5029-0.3324-0.09510.56220.67860.1052-0.36780.2247-0.01740.03640.3701-0.0690.3514-9.0109-34.2875-27.6762
69.1386-5.65087.66347.4202-4.74878.9647-0.18630.2999-0.27090.0090.0003-0.0553-0.04120.31610.09520.1851-0.03230.01740.2814-0.03970.2966-0.5969-32.4731-28.9523
70.18470.3140.7630.86541.4424.29910.06840.059-0.21350.16090.13520.0316-0.13980.0608-0.16110.24310.04130.03560.3953-0.03780.27960.0487-27.9325-28.1192
86.3561.74253.87087.18936.83947.5399-0.2091-0.575-0.36191.02810.1650.42730.6769-0.5750.0010.4444-0.01210.10830.33870.11170.3004-8.8147-27.0605-6.7574
93.36672.95583.96418.16467.02796.29010.2891-0.2491-0.36530.7717-0.27960.11941.0637-0.99220.01940.2914-0.02680.03940.34590.00920.3372-14.425-27.4951-18.8544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 37 )A15 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 58 )A38 - 58
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 127 )A59 - 127
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 168 )A128 - 168
5X-RAY DIFFRACTION5chain 'A' and (resid 169 through 189 )A169 - 189
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 208 )A190 - 208
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 222 )A209 - 222
8X-RAY DIFFRACTION8chain 'A' and (resid 223 through 243 )A223 - 243
9X-RAY DIFFRACTION9chain 'A' and (resid 244 through 263 )A244 - 263

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