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- PDB-4m3p: Betaine-Homocysteine S-Methyltransferase from Homo sapiens comple... -

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Basic information

Entry
Database: PDB / ID: 4m3p
TitleBetaine-Homocysteine S-Methyltransferase from Homo sapiens complexed with Homocysteine
ComponentsBetaine--homocysteine S-methyltransferase 1
KeywordsTRANSFERASE / Alpha and beta proteins (a/b) / TIM beta/alpha-barrel / methyltransferase activity / homocysteine S-methyltransferase activity / transferase activity / metal ion binding / betaine-homocysteine S-methyltransferase activity / protein complex binding / betaine / homocysteine
Function / homology
Function and homology information


regulation of homocysteine metabolic process / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / amino-acid betaine catabolic process / Sulfur amino acid metabolism / Choline catabolism / 'de novo' L-methionine biosynthetic process / protein methylation ...regulation of homocysteine metabolic process / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / amino-acid betaine catabolic process / Sulfur amino acid metabolism / Choline catabolism / 'de novo' L-methionine biosynthetic process / protein methylation / extracellular exosome / zinc ion binding / nucleus / cytosol
Similarity search - Function
Betaine-homocysteine S-methyltransferase, BHMT / Homocysteine-binding-like domain / Homocysteine-binding domain / Homocysteine-binding domain superfamily / Homocysteine S-methyltransferase / Homocysteine-binding domain profile. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-AMINO-4-MERCAPTO-BUTYRIC ACID / : / S,R MESO-TARTARIC ACID / Betaine--homocysteine S-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsKoutmos, M. / Yamada, K. / Mladkova, J. / Paterova, J. / Diamond, C.E. / Tryon, K. / Jungwirth, P. / Garrow, T.A. / Jiracek, J.
CitationJournal: Proteins / Year: 2014
Title: Specific potassium ion interactions facilitate homocysteine binding to betaine-homocysteine S-methyltransferase.
Authors: Mladkova, J. / Hladilkova, J. / Diamond, C.E. / Tryon, K. / Yamada, K. / Garrow, T.A. / Jungwirth, P. / Koutmos, M. / Jiracek, J.
History
DepositionAug 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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_2
Revision 2.1Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Betaine--homocysteine S-methyltransferase 1
B: Betaine--homocysteine S-methyltransferase 1
C: Betaine--homocysteine S-methyltransferase 1
D: Betaine--homocysteine S-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,38018
Polymers180,1224
Non-polymers1,25914
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20430 Å2
ΔGint-76 kcal/mol
Surface area54010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.097, 102.617, 96.228
Angle α, β, γ (deg.)90.00, 101.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Betaine--homocysteine S-methyltransferase 1


Mass: 45030.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BHMT / Plasmid: pTYB4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q93088, betaine-homocysteine S-methyltransferase

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Non-polymers , 5 types, 658 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine / Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9NO2S
#5: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsR239Q IS A NATURAL VARIANT.

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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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.5
Details: 20.0% PEG5000 MME, 0.2 M sodium/potassium tartrate, 1.4% 1,2,3-heptanetriol, pH 7.5, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2006
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.895→45.222 Å / Num. all: 129862 / Num. obs: 128582 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.072 / Net I/σ(I): 13.7
Reflection shellResolution: 1.895→2.01 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4 / Num. unique all: 19787 / Rsym value: 0.369 / % possible all: 90

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Processing

Software
NameVersionClassification
Blu-Icedata collection
EPMRphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LT8

1lt8


Resolution: 1.895→45.222 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.334 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.142 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21852 6476 5 %RANDOM
Rwork0.18021 ---
obs0.18214 122106 99.01 %-
all-123327 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.943 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20.42 Å2
2--2.05 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 1.895→45.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11469 0 60 644 12173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911821
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211346
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.95915983
X-RAY DIFFRACTIONr_angle_other_deg0.806325980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51651463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21824.063539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.009151989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9511572
X-RAY DIFFRACTIONr_chiral_restr0.0820.21687
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113392
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022636
LS refinement shellResolution: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 395 -
Rwork0.246 7870 -
obs--87.71 %

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