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- PDB-5h02: Crystal structure of Methanohalophilus portucalensis glycine sarc... -

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Basic information

Entry
Database: PDB / ID: 5h02
TitleCrystal structure of Methanohalophilus portucalensis glycine sarcosine N-methyltransferase tetramutant (H21G, E23T, E24N, L28S)
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


cellular nitrogen compound metabolic process / glycine N-methyltransferase activity / organic substance biosynthetic process / cellular biosynthetic process / methylation
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 / 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: 1.776 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
DepositionOct 2, 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
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)33,1404
Polymers32,5191
Non-polymers6213
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.874, 120.803, 131.301
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-424-

HOH

21A-437-

HOH

31A-495-

HOH

41A-548-

HOH

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Components

#1: Protein Glycine sarcosine N-methyltransferase


Mass: 32518.896 Da / Num. of mol.: 1 / Mutation: H21G, E23T, E24N, L28S
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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-BET / TRIMETHYL GLYCINE / Trimethylglycine


Mass: 118.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 61.11 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / 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 50 mM glycine. Crystallization reagent: 0.2 M Ammonium phosphate monobasic. ...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 50 mM glycine. Crystallization reagent: 0.2 M Ammonium phosphate monobasic. 0.23 M ammonia phosphate monobasic, 0.1 mM SAH and 3.35 M betaine were used as cryoprotectant 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 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.776→20 Å / Num. obs: 40112 / % possible obs: 100 % / Redundancy: 4.9 % / Net I/σ(I): 31.518
Reflection shellResolution: 1.78→1.82 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Blu-Icedata collection
HKL-2000data scaling
HKL-2000data processing
PHENIX1.8_1069model building
HKL-2000data reduction
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HIL

5hil


Resolution: 1.776→19.888 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.88
RfactorNum. reflection% reflection
Rfree0.1958 1995 4.97 %
Rwork0.1765 --
obs0.1775 40110 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.776→19.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 42 173 2222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062102
X-RAY DIFFRACTIONf_angle_d0.7962849
X-RAY DIFFRACTIONf_dihedral_angle_d16.0151214
X-RAY DIFFRACTIONf_chiral_restr0.053299
X-RAY DIFFRACTIONf_plane_restr0.004372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7758-1.82010.21751340.2242584X-RAY DIFFRACTION96
1.8201-1.86930.22911300.21712688X-RAY DIFFRACTION100
1.8693-1.92430.24521640.20792681X-RAY DIFFRACTION100
1.9243-1.98630.24841270.2032718X-RAY DIFFRACTION100
1.9863-2.05720.20421500.19082691X-RAY DIFFRACTION100
2.0572-2.13950.22321380.18332705X-RAY DIFFRACTION100
2.1395-2.23680.22031380.17572722X-RAY DIFFRACTION100
2.2368-2.35450.20711430.17372711X-RAY DIFFRACTION100
2.3545-2.50180.20931450.19052725X-RAY DIFFRACTION100
2.5018-2.69450.21731450.18612723X-RAY DIFFRACTION100
2.6945-2.96490.19531460.18772735X-RAY DIFFRACTION100
2.9649-3.39210.19021390.16782755X-RAY DIFFRACTION100
3.3921-4.26670.16081480.14822785X-RAY DIFFRACTION100
4.2667-19.88890.1841480.17392892X-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)
11.7202-2.3068-0.1217.7484-4.69735.077-0.21520.36510.2393-0.51830.42791.1911-0.5434-0.6531-0.27010.37060.0122-0.10720.35830.08460.390446.671145.9382160.8828
26.7253-0.4716-5.46931.74880.39465.7188-0.089-0.2465-0.12180.23470.2472-0.50910.58611.03840.03680.24640.0253-0.07140.30340.00840.339768.705645.1121154.1731
33.2852-0.1079-0.52252.68721.91513.6681-0.07560.27680.2164-0.21490.0389-0.0072-0.22880.10490.0330.1847-0.0158-0.01410.12130.05890.155155.90852.9646149.3583
42.4916-0.13591.3296.3956-1.30333.7689-0.110.3098-0.0286-0.31570.01080.04330.0291-0.04590.08490.129-0.00450.00470.2395-0.01760.102454.523840.3117141.8861
52.13270.4075-0.19652.44451.70897.2330.02530.0428-0.35010.14910.014-0.14880.5159-0.0733-0.04890.1490.00890.00550.16610.05020.209454.894528.0235159.3831
62.4747-0.31513.07671.9131-2.11496.89760.04250.3917-0.2139-0.3113-0.0262-0.16750.25170.3140.02780.16370.02450.04030.2229-0.03180.154463.169132.8932144.4546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 127 )
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 167 )
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 222 )
6X-RAY DIFFRACTION6chain 'A' and (resid 223 through 263 )

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