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- PDB-9yce: Active site of MtgB, a glycine betaine methyltransferase from the... -

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Basic information

Entry
Database: PDB / ID: 9yce
TitleActive site of MtgB, a glycine betaine methyltransferase from the MttB superfamily
ComponentsGlycine betaine methyltransferase
KeywordsTRANSFERASE / bacterial metabolism / microbiology / energy metabolism / folate / microbiome / enzyme catalysis / cobalamin / one carbon metabolism / glycine betaine / methyltransferase / Desulfitobacterium
Function / homology
Function and homology information


glycine betaine-corrinoid protein Co-methyltransferase / methanogenesis / one-carbon metabolic process / methyltransferase activity / methylation
Similarity search - Function
Trimethylamine methyltransferase / MttB-like superfamily / Trimethylamine methyltransferase (MTTB)
Similarity search - Domain/homology
TRIMETHYL GLYCINE / IMIDAZOLE / Glycine betaine methyltransferase
Similarity search - Component
Biological speciesDesulfitobacterium hafniense Y51 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPicking, J. / Li, Y. / Ticak, T. / Ferguson, D.J. / Hao, B. / Krzycki, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135592 United States
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Delineation of the active site of MtgB, a cobalamin-dependent glycine betaine methyltransferase.
Authors: Picking, J. / Li, Y. / Ticak, T. / Ferguson, D.J. / Hao, B. / Krzycki, J.A.
History
DepositionSep 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine betaine methyltransferase
B: Glycine betaine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1546
Polymers104,7872
Non-polymers3674
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-72 kcal/mol
Surface area30800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.465, 123.465, 123.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glycine betaine methyltransferase / GB methyltransferase / Glycine betaine--corrinoid protein Co-methyltransferase / Glycine betaine: ...GB methyltransferase / Glycine betaine--corrinoid protein Co-methyltransferase / Glycine betaine:cob(I)alamin methyltransferase / Glycine betaine:corrinoid methyltransferase


Mass: 52393.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense Y51 (bacteria)
Gene: mtgB, DSY3156 / Plasmid: pSpeedET / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q24SP7, glycine betaine-corrinoid protein Co-methyltransferase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-BET / TRIMETHYL GLYCINE


Mass: 118.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Imidazole, 1.0 M sodium citrate, pH 8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS-II 17-ID-111.075
SYNCHROTRONNSLS-II 17-ID-221.075
Detector
TypeIDDetectorDate
DECTRIS EIGER X 9M1PIXELFeb 14, 2019
DECTRIS EIGER X 16M2PIXELMay 14, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0751
21
ReflectionResolution: 2.349→106.924 Å / Num. obs: 45582 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 21.3 % / Biso Wilson estimate: 65.14 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.021 / Rrim(I) all: 0.097 / Net I/σ(I): 21.3
Reflection shellResolution: 2.349→2.389 Å / Redundancy: 22.5 % / Rmerge(I) obs: 1.251 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2253 / CC1/2: 0.909 / Rpim(I) all: 0.269 / Rrim(I) all: 1.288 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
autoPROCdata scaling
autoPROCdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→34.26 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.309 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.31 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.205
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2157 4.73 %RANDOM
Rwork0.191 ---
obs0.192 45568 99.5 %-
Displacement parametersBiso mean: 79.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.8238 Å20 Å20 Å2
2---0.8238 Å20 Å2
3---1.6477 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 2.35→34.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7180 0 0 233 7413
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087377HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.029984HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3400SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1272HARMONIC5
X-RAY DIFFRACTIONt_it7377HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion2.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion971SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8935SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.37 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2521 -2.96 %
Rwork0.2222 885 -
all0.2231 912 -
obs--100 %
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)
10.75440.12570.12622.40681.26691.7850.038-0.12410.024-0.0643-0.22860.2381-0.1151-0.31720.1907-0.1234-0.0222-0.034-0.0803-0.1221-0.116628.7074-26.74171.3015
20.98390.4099-0.04672.99241.50082.08130.1264-0.2466-0.43381.11470.1974-0.91181.01550.4182-0.32380.16340.1431-0.3462-0.2779-0.0082-0.009548.3953-54.440612.2252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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