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

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Basic information

Entry
Database: PDB / ID: 5hik
TitleCrystal structure of glycine sarcosine N-methyltransferase from Methanohalophilus portucalensis in complex with S-adenosylmethionine
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


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 / Class I SAM-dependent methyltransferase
Similarity search - Component
Biological speciesMethanohalophilus portucalensis FDF-1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.354 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)33,4476
Polymers32,8001
Non-polymers6475
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint15 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.906, 120.970, 131.789
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-423-

HOH

21A-425-

HOH

31A-430-

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-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 73 / 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: 61 %
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. SAM was 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 18, 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: 2.35→30 Å / Num. obs: 17545 / % possible obs: 99.9 % / Redundancy: 4.6 % / Rsym value: 0.063 / Net I/σ(I): 22.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.9 / % 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 5HIL

5hil


Resolution: 2.354→27.486 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 877 5 %Random selection
Rwork0.1662 ---
obs0.1686 17543 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.354→27.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 43 73 2075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072050
X-RAY DIFFRACTIONf_angle_d1.0352766
X-RAY DIFFRACTIONf_dihedral_angle_d13.675739
X-RAY DIFFRACTIONf_chiral_restr0.043289
X-RAY DIFFRACTIONf_plane_restr0.004358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3539-2.50130.261330.19192675X-RAY DIFFRACTION98
2.5013-2.69430.27831500.19312734X-RAY DIFFRACTION100
2.6943-2.96510.25871410.19932756X-RAY DIFFRACTION100
2.9651-3.39350.21441450.17962793X-RAY DIFFRACTION100
3.3935-4.27290.19941470.14682800X-RAY DIFFRACTION100
4.2729-27.48780.18971610.15172908X-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)
13.4014-2.94233.28293.1588-1.47996.1897-0.341-0.30030.2310.30170.4332-0.5648-0.73670.082-0.1060.40410.0285-0.01920.3694-0.08650.42453.6723-17.7949-32.5538
27.5265-1.7575-5.83445.07471.64384.937-0.18320.6742-0.5913-0.2608-0.14770.90640.1811-1.5760.34230.27630.0265-0.02220.4958-0.06930.6037-17.3738-14.5247-22.3808
35.20350.8263-1.76912.8259-1.31956.2921-0.1534-0.11970.03980.06520.1750.3557-0.31-0.3214-0.00920.27880.0421-0.02420.2048-0.00720.2935-8.8715-8.3991-18.2351
45.5316-6.89484.91152.0099-3.3949.58150.45950.8290.0679-1.1213-0.3189-0.05050.15550.1297-0.10920.3826-0.0788-0.0130.23420.02790.3314-1.138-5.2765-28.1548
59.0071-7.56466.80719.1476-7.18725.8897-0.61990.16410.07021.00540.341-0.1487-1.01170.11990.33890.3311-0.0248-0.01610.3079-0.01150.32160.5726-7.4667-16.1455
64.6562-0.84510.84117.54972.40335.4946-0.236-0.2119-0.03810.76470.31760.0223-0.00910.3244-0.07090.28930.04580.02570.30110.02720.1845-2.7889-17.5414-10.1125
71.60290.3921-0.45783.5248-0.68688.6713-0.15160.0807-0.2359-0.08580.13130.06810.4033-0.0913-0.0080.17790.0160.00870.2865-0.05420.3307-3.3361-31.63-28.2896
87.62541.03973.62733.79422.84725.6682-0.1618-0.7326-0.51541.16540.17950.6890.2875-0.4664-0.0730.64010.0760.13140.32340.12160.3026-8.735-27.0962-6.8306
93.1512.56543.74376.20465.37335.64510.1793-0.3719-0.46310.6301-0.4190.60540.4848-1.06490.25580.2727-0.02120.08830.32630.02540.4238-14.3281-27.602-19.0518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 120 )
6X-RAY DIFFRACTION6chain 'A' and (resid 121 through 167 )
7X-RAY DIFFRACTION7chain 'A' and (resid 168 through 222 )
8X-RAY DIFFRACTION8chain 'A' and (resid 223 through 243 )
9X-RAY DIFFRACTION9chain 'A' and (resid 244 through 263 )

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