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- PDB-5hii: Crystal structure of glycine sarcosine N-methyltransferase (GSMT)... -

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Basic information

Entry
Database: PDB / ID: 5hii
TitleCrystal structure of glycine sarcosine N-methyltransferase (GSMT) from Methanohalophilus portucalensis (apo form)
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
Class I SAM-dependent methyltransferase
Similarity search - Component
Biological speciesMethanohalophilus portucalensis FDF-1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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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)33,1737
Polymers32,8001
Non-polymers3726
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint17 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.729, 120.450, 130.941
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-455-

HOH

21A-460-

HOH

31A-487-

HOH

41A-534-

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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 155 / 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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: Protein solution: GSMT (6.6 mg/ml) in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 1 mM EDTA and 1 mM 2-Mercaptoethanol. Crystallization reagent: 0.1 M Tris-HCl pH 8.5, 0.2 M sodium chloride, 25% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 23, 2011
RadiationMonochromator: Horizontally Focusing Single Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 32198 / % possible obs: 99.2 % / Redundancy: 5.4 % / Rsym value: 0.052 / Net I/σ(I): 27.6
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.9 / % 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: 1.9→28.544 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 1614 5.01 %Random
Rwork0.1706 ---
obs0.1719 32198 98.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→28.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 24 155 2152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062037
X-RAY DIFFRACTIONf_angle_d0.9382738
X-RAY DIFFRACTIONf_dihedral_angle_d13.42733
X-RAY DIFFRACTIONf_chiral_restr0.041284
X-RAY DIFFRACTIONf_plane_restr0.004357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.9560.28331270.22532300X-RAY DIFFRACTION91
1.956-2.01910.2491330.20412567X-RAY DIFFRACTION100
2.0191-2.09120.24591300.18962550X-RAY DIFFRACTION100
2.0912-2.17490.20841470.17562539X-RAY DIFFRACTION100
2.1749-2.27390.19811210.16822584X-RAY DIFFRACTION100
2.2739-2.39370.19581430.17162532X-RAY DIFFRACTION100
2.3937-2.54360.20411280.17512579X-RAY DIFFRACTION100
2.5436-2.73980.23831380.18392588X-RAY DIFFRACTION99
2.7398-3.01530.20471380.18362562X-RAY DIFFRACTION100
3.0153-3.4510.16261370.16652592X-RAY DIFFRACTION99
3.451-4.34540.15621360.14962575X-RAY DIFFRACTION98
4.3454-28.54740.21511360.1672616X-RAY DIFFRACTION95
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)
18.0736-3.28323.83682.7953-0.49919.2906-0.32010.52230.4638-0.21430.3125-0.6094-0.31060.57890.00520.3001-0.02830.00210.2312-0.07880.293855.080542.621233.4467
26.67710.5365-4.47882.62620.39983.85190.07360.4231-0.3429-0.3852-0.03420.45320.1872-1.3906-0.02360.27360.0123-0.09920.45160.00260.510634.00246.052441.998
35.61580.2891-2.21072.6708-0.44555.2293-0.06730.01010.0575-0.08170.03420.1741-0.2809-0.14290.02260.21450.01-0.03190.1368-0.02690.178444.773352.723844.7772
46.1093-3.7174.40928.2823-5.21187.706-0.2479-0.1730.17570.4263-0.0013-0.13-0.4130.17320.25780.153-0.02380.02830.1643-0.01390.120751.410353.197247.9384
54.1678-1.89560.60596.44611.54373.0511-0.09730.02940.1170.20020.1627-0.24330.00010.2039-0.0890.1559-0.01010.00830.23810.01520.152151.606643.699455.5596
63.34410.53180.69464.77392.02953.91750.05070.1063-0.29590.2166-0.24290.27110.4097-0.34350.27390.1531-0.030.01240.25540.0220.146243.14733.266649.7565
71.8672-0.11260.63423.0606-0.39694.34240.03020.1431-0.1868-0.19710.07260.20240.3286-0.0049-0.0990.2236-0.01250.01510.2808-0.05160.256548.94830.20335.8126
87.63510.36133.55445.99644.03536.0038-0.2599-0.5089-0.26850.69190.13260.38130.4565-0.45640.14140.3331-0.00090.07940.26790.06730.172742.775533.383959.1604
94.07871.88765.0083.59274.18115.76940.1877-0.2205-0.39330.3595-0.12950.0790.5196-0.635-0.01890.2356-0.02850.03660.27640.00680.253737.040232.862546.6834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 117 )
5X-RAY DIFFRACTION5chain 'A' and (resid 118 through 155 )
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 182 )
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 222 )
8X-RAY DIFFRACTION8chain 'A' and (resid 223 through 243 )
9X-RAY DIFFRACTION9chain 'A' and (resid 244 through 263 )

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