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- PDB-4ndn: Structural insights of MAT enzymes: MATa2b complexed with SAM and PPNP -

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Basic information

Entry
Database: PDB / ID: 4ndn
TitleStructural insights of MAT enzymes: MATa2b complexed with SAM and PPNP
Components
  • Methionine adenosyltransferase 2 subunit betaS-Adenosylmethionine synthetase enzyme
  • S-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE / S-adenosylmethionine (SAMe) synthesis
Function / homology
Function and homology information


methionine adenosyltransferase regulator activity / methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor ...methionine adenosyltransferase regulator activity / methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process / Ub-specific processing proteases / enzyme binding / extracellular exosome / ATP binding / identical protein binding / metal ion 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
(DIPHOSPHONO)AMINOPHOSPHONIC ACID / 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: 2.34 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
DepositionOct 27, 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 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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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)250,24431
Polymers247,7816
Non-polymers2,46325
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18530 Å2
ΔGint-69 kcal/mol
Surface area74660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.140, 122.178, 298.423
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 43720.625 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 / S-Adenosylmethionine synthetase enzyme / Methionine adenosyltransferase II beta / MAT II beta / Putative dTDP-4-keto-6-deoxy-D-glucose 4-reductase


Mass: 36449.348 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, 523 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PPK / (DIPHOSPHONO)AMINOPHOSPHONIC ACID


Mass: 256.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H6NO9P3
#6: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MES/Imidazole buffer 10% Ethylene glycol 20% PEG 8K, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 109240 / % possible obs: 98 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.101 / Χ2: 0.956 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.435.20.70491580.874183.2
2.43-2.536.30.785107210.879197.5
2.53-2.657.60.707110240.889199.8
2.65-2.798.20.512110560.898199.7
2.79-2.967.80.334109910.949199.8
2.96-3.198.20.221110590.999199.9
3.19-3.517.90.125111381.041199.9
3.51-4.028.20.076111791.006199.9
4.02-5.067.90.053112541.019199.9
5.06-507.70.045116600.942199.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→47.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2448 / WRfactor Rwork: 0.2047 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7978 / SU B: 9.002 / SU ML: 0.202 / SU R Cruickshank DPI: 0.3578 / SU Rfree: 0.2462 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 5409 5 %RANDOM
Rwork0.2106 ---
obs0.2126 108283 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.44 Å2 / Biso mean: 57.3271 Å2 / Biso min: 26.69 Å2
Baniso -1Baniso -2Baniso -3
1-4.42 Å20 Å20 Å2
2--2.38 Å20 Å2
3----6.8 Å2
Refinement stepCycle: LAST / Resolution: 2.34→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16439 0 152 498 17089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01916946
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216325
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.96422928
X-RAY DIFFRACTIONr_angle_other_deg0.696337546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71152097
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.223.792770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45152898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.74115121
X-RAY DIFFRACTIONr_chiral_restr0.0580.22531
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02119101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023858
LS refinement shellResolution: 2.344→2.404 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 285 -
Rwork0.369 5551 -
all-5836 -
obs--70.97 %

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