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- PDB-4ktt: Structural insights of MAT enzymes: MATa2b complexed with SAM -

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Basic information

Entry
Database: PDB / ID: 4ktt
TitleStructural insights of MAT enzymes: MATa2b complexed with SAM
Components
  • Methionine adenosyltransferase 2 subunit beta
  • S-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE / SAMe Synthesis
Function / homology
Function and homology information


methionine adenosyltransferase regulator activity / methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / cellular response to methionine / protein hexamerization / small molecule binding ...methionine adenosyltransferase regulator activity / methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / cellular response to methionine / protein hexamerization / small molecule binding / one-carbon metabolic process / positive regulation of TORC1 signaling / cellular response to leukemia inhibitory factor / Ub-specific processing proteases / enzyme binding / extracellular exosome / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate binding domain / GMP Synthetase; Chain A, domain 3 - #10 / S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily ...dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate binding domain / GMP Synthetase; Chain A, domain 3 - #10 / S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthase signature 1. / S-adenosylmethionine synthase signature 2. / GMP Synthetase; Chain A, domain 3 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase isoform type-2 / Methionine adenosyltransferase 2 subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsMurray, B. / Antonyuk, S.V. / Marina, A. / Lu, S.C. / Mato, J.M. / Hasnain, S.S. / Rojas, A.L.
CitationJournal: IUCrJ / Year: 2014
Title: Structure and function study of the complex that synthesizes S-adenosylmethionine.
Authors: Murray, B. / Antonyuk, S.V. / Marina, A. / Van Liempd, S.M. / Lu, S.C. / Mato, J.M. / Hasnain, S.S. / Rojas, A.L.
History
DepositionMay 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Structure summary
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 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_ref_seq_dif / 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_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.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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine synthase isoform type-2
B: S-adenosylmethionine synthase isoform type-2
C: S-adenosylmethionine synthase isoform type-2
D: S-adenosylmethionine synthase isoform type-2
E: Methionine adenosyltransferase 2 subunit beta
F: Methionine adenosyltransferase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,70539
Polymers248,9566
Non-polymers2,74933
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17920 Å2
ΔGint-63 kcal/mol
Surface area73450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.442, 115.723, 298.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein
S-adenosylmethionine synthase isoform type-2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2 / Methionine adenosyltransferase II / MAT-II


Mass: 43807.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P31153, methionine adenosyltransferase
#2: Protein Methionine adenosyltransferase 2 subunit beta / Methionine adenosyltransferase II beta / MAT II beta / Putative dTDP-4-keto-6-deoxy-D-glucose 4-reductase


Mass: 36862.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2B, TGR, MSTP045, Nbla02999, UNQ2435/PRO4995 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZL9

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Non-polymers , 5 types, 141 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE DATABASE SEQEUNCE REFEREENCE FOR METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA IS Q9NZL9 ...THE DATABASE SEQEUNCE REFEREENCE FOR METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA IS Q9NZL9 ISOFORM 2. THE SEQUENCE OF THIS ISOFORM DIFFERS FROM THE CANONICAL SEQUENCE AS FOLLOWS: RESIDUES 1-21: MVGREKELSIHFVPGSCRLVE TO MPEMPEDMEQ.

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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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 0.1M MES/Imidazole pH 6.5 0.1M Carboxylic acids 20% Ethylene glycol 10% PEG 8K, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 78380 / Num. obs: 77361 / % possible obs: 98.7 % / Observed criterion σ(F): 1.75 / Observed criterion σ(I): 1.75 / Redundancy: 5.6 % / Rmerge(I) obs: 0.144
Reflection shellResolution: 2.6→2.69 Å / % possible all: 90.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2PO2 AND 2YDY

2po2

2ydy


Resolution: 2.59→47.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.52 / SU B: 12.967 / SU ML: 0.275 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflection
Rfree0.279 3847 5 %
Rwork0.218 --
obs0.221 76590 96.8 %
all-78380 -
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 75.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.29 Å20 Å20 Å2
2---0.06 Å20 Å2
3----3.23 Å2
Refinement stepCycle: LAST / Resolution: 2.59→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16216 0 177 108 16501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01916705
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216113
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.96322558
X-RAY DIFFRACTIONr_angle_other_deg0.71337052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88452053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1923.834759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55152854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.33715116
X-RAY DIFFRACTIONr_chiral_restr0.060.22490
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023791
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.66 Å
RfactorNum. reflection% reflection
Rfree0.35 237 -
Rwork0.294 4091 -
obs--75.59 %

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