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- PDB-7rxv: Human Methionine Adenosyltransferase 2A bound to Methylthioadenos... -

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Basic information

Entry
Database: PDB / ID: 7rxv
TitleHuman Methionine Adenosyltransferase 2A bound to Methylthioadenosine, Malonate (MLA) and MgF3
ComponentsS-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SAM SYNTHETASE / ENZYME MECHANISM / INHIBITOR / TRANSITION STATE / TRANSFERASE-INHIBITOR COMPLEX / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


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 ...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 / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
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.
Similarity search - Domain/homology
ALANINE / : / TRIFLUOROMAGNESATE / MALONIC ACID / 5'-DEOXY-5'-METHYLTHIOADENOSINE / S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.07 Å
AuthorsFedorov, E. / Niland, C.N. / Schramm, V.L. / Ghosh, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM041916 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA013330 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Mechanism of Triphosphate Hydrolysis by Human MAT2A at 1.07 angstrom Resolution.
Authors: Ghosh, A. / Niland, C.N. / Cahill, S.M. / Karadkhelkar, N.M. / Schramm, V.L.
History
DepositionAug 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,05310
Polymers46,2791
Non-polymers7739
Water6,864381
1
A: S-adenosylmethionine synthase isoform type-2
hetero molecules

A: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,10520
Polymers92,5592
Non-polymers1,54718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10140 Å2
ΔGint-67 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.981, 94.122, 117.315
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-711-

HOH

21A-876-

HOH

31A-901-

HOH

41A-981-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 46279.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31153, methionine adenosyltransferase

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Non-polymers , 9 types, 390 molecules

#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4% Tacsimate (1.83 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M sodium acetate trihydrate, 0.5 M sodium formate, and 0.16 M ammonium ...Details: 4% Tacsimate (1.83 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M sodium acetate trihydrate, 0.5 M sodium formate, and 0.16 M ammonium tartrate dibasic) and 12% PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2020 / Details: KB MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.07→19.86 Å / Num. obs: 153643 / % possible obs: 93.2 % / Redundancy: 11.4 % / Biso Wilson estimate: 10.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.017 / Rrim(I) all: 0.061 / Net I/σ(I): 21.4 / Num. measured all: 1748608 / Scaling rejects: 710
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.07-1.095.10.572200642830.8220.2720.6352.952.9
5.86-19.8612.60.0431368710850.9980.0130.04551.297.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.85 Å19.86 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.19rc5_4047refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L1A

7l1a


Resolution: 1.07→19.86 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 13.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1387 7718 5.02 %
Rwork0.1295 145905 -
obs0.13 153623 93.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.47 Å2 / Biso mean: 14.2341 Å2 / Biso min: 6.83 Å2
Refinement stepCycle: final / Resolution: 1.07→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 31 402 3413
Biso mean--25.22 23.35 -
Num. residues----382
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.07-1.080.2321430.23652612275550
1.08-1.090.2131490.2143071322059
1.09-1.110.20921920.193388358066
1.11-1.120.17551880.1773760394872
1.12-1.140.17772100.16854154436480
1.14-1.150.1842240.16134460468486
1.15-1.170.16432440.15454694493891
1.17-1.190.1632680.14934879514794
1.19-1.210.15342860.14475103538999
1.21-1.220.14992640.137451745438100
1.22-1.250.16662800.132951735453100
1.25-1.270.1432450.133152435488100
1.27-1.290.13192850.131651815466100
1.29-1.320.14282550.131551955450100
1.32-1.350.14172740.133751705444100
1.35-1.380.14093030.128951655468100
1.38-1.410.13853050.12751825487100
1.41-1.450.14652700.129351995469100
1.45-1.490.13612440.123352425486100
1.49-1.540.13252720.123151875459100
1.54-1.60.12592720.119452055477100
1.6-1.660.14032940.120151995493100
1.66-1.740.13322770.123552215498100
1.74-1.830.14132760.126552355511100
1.83-1.940.12763000.126951885488100
1.94-2.090.12542680.121452625530100
2.09-2.30.12382810.121752815562100
2.3-2.640.14082470.123553065553100
2.64-3.320.133110.130152885599100
3.32-19.860.13862910.125654885779100
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)
13.34754.20381.51856.2627-0.98279.18640.11141.4425-0.3666-1.2807-0.1928-0.38830.2570.10370.05070.23130.0030.03050.2201-0.02050.10156.203-12.108-47.858
20.3179-0.1118-0.16040.38390.08930.5269-0.0276-0.0409-0.00740.04480.02620.04440.0052-0.04230.00330.07560.00280.00220.08690.00570.0849-10.131-4.729-13.534
35.4016-1.8876-1.29475.47752.62996.8915-0.10210.1098-0.1547-0.0017-0.02070.34490.0958-0.47640.15560.0688-0.01680.01030.11750.01340.0826-11.828-14.12-7.204
40.0976-0.126-0.01050.55820.01220.3888-0.007-0.0074-0.01410.00810.00410.04580.0102-0.04020.00370.053-0.0161-0.00040.0861-0.00020.0924-9.326-7.67-20.13
51.6405-0.0102-0.39921.448-0.32122.8279-0.04520.1597-0.0123-0.1792-0.0496-0.03060.02920.12020.08170.0824-0.00020.00230.0404-0.01960.081.856-15.56-36.189
60.4015-0.22870.05680.5542-0.05090.3118-0.00220.0122-0.0489-0.04290.0140.00030.05320.0146-0.01240.088-0.0073-0.00080.0832-0.00470.08931.389-16.242-27.15
70.4481-0.1468-0.03520.6012-0.00370.40120.00540.0551-0.0181-0.10630.00090.08590.0076-0.0636-0.00970.0931-0.0071-0.01460.0862-0.00420.087-15.808-0.845-36.246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 16:18 )A16 - 18
2X-RAY DIFFRACTION2( CHAIN A AND RESID 19:80 )A19 - 80
3X-RAY DIFFRACTION3( CHAIN A AND RESID 81:89 )A81 - 89
4X-RAY DIFFRACTION4( CHAIN A AND RESID 90:176 )A90 - 176
5X-RAY DIFFRACTION5( CHAIN A AND RESID 177:192 )A177 - 192
6X-RAY DIFFRACTION6( CHAIN A AND RESID 193:296 )A193 - 296
7X-RAY DIFFRACTION7( CHAIN A AND RESID 297:395 )A297 - 395

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