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

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Basic information

Entry
Database: PDB / ID: 7rxx
TitleHuman Methionine Adenosyltransferase 2A bound to Methylthioadenosine and two sulfate in the active site
ComponentsS-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SAM SYNTHETASE / ENZYME MECHANISM / 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 / : / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 3,6,9,12,15-PENTAOXAHEPTADECANE / S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 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 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,35014
Polymers46,2791
Non-polymers1,07113
Water6,630368
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)94,70028
Polymers92,5592
Non-polymers2,14126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area11440 Å2
ΔGint-188 kcal/mol
Surface area24250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.224, 94.121, 117.159
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-613-

HOH

21A-780-

HOH

31A-796-

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, 381 molecules

#2: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O5
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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.: 4 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 39.47 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 200 mM potassium sulfate and 20% 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: 1.25→19.88 Å / Num. obs: 103477 / % possible obs: 99.5 % / Redundancy: 12.9 % / Biso Wilson estimate: 7.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.027 / Rrim(I) all: 0.098 / Net I/σ(I): 18.8 / Num. measured all: 1330026 / Scaling rejects: 415
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
1.25-1.2712.70.5516441250690.9490.1610.5756.199.7
6.85-19.8812.60.05385916810.9950.0150.05539.395.8

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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: 1.25→19.88 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 11.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1405 5202 5.03 %
Rwork0.1291 98263 -
obs0.1297 103465 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.11 Å2 / Biso mean: 11.4753 Å2 / Biso min: 3.9 Å2
Refinement stepCycle: final / Resolution: 1.25→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 115 394 3463
Biso mean--14.44 21.25 -
Num. residues----380
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 (%)
1.25-1.260.16411570.16432433400100
1.26-1.280.16341690.149832253394100
1.28-1.290.17941850.14563264344999
1.29-1.310.15341760.14443155333197
1.31-1.330.1451590.14283225338499
1.33-1.350.15941980.140832373435100
1.35-1.370.14241540.142732903444100
1.37-1.390.14031630.132932533416100
1.39-1.410.13631720.134532823454100
1.41-1.430.1431780.136332403418100
1.43-1.460.13461650.12632843449100
1.46-1.480.13151670.12233259342699
1.48-1.510.14821640.12343224338898
1.51-1.540.13951530.11973207336098
1.54-1.570.13021740.116632583432100
1.57-1.610.12321580.116533163474100
1.61-1.650.12531860.118432953481100
1.65-1.70.1331740.116432413415100
1.7-1.750.13491890.117532903479100
1.75-1.80.14581800.121232793459100
1.8-1.870.13241680.12293251341999
1.87-1.940.1312040.12433196340098
1.94-2.030.12061650.122533053470100
2.03-2.140.14461750.122933133488100
2.14-2.270.13191720.12133243496100
2.27-2.450.13351730.12333203493100
2.45-2.690.13331670.13313301346899
2.69-3.080.15661760.133133563532100
3.08-3.870.14391850.131733573542100
3.88-19.880.14471960.13663473366999
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)
15.2755-2.0431-3.17115.25484.06956.87770.05840.5407-0.0377-0.4235-0.007-0.1239-0.1192-0.0093-0.05180.1561-0.01510.02340.1367-0.0050.07146.2645-12.1554-47.833
20.2241-0.062-0.07060.2845-0.00330.3234-0.0342-0.0517-0.00610.05090.02820.03510.0112-0.02610.00340.0560.00740.00290.06930.00290.0641-10.176-4.655-13.5141
32.0628-1.03-0.70993.92580.85672.4584-0.07330.0424-0.1238-0.0220.0620.24870.0488-0.3160.03790.061-0.00590.0090.11120.00680.0757-11.9566-14.0433-7.1823
40.0951-0.112-0.00920.5594-0.01520.3628-0.0098-0.0162-0.01390.01810.00390.04070.0117-0.03590.00510.0358-0.01460.00020.0723-0.00090.076-9.27-7.8492-20.2373
50.8185-0.0177-0.21180.7569-0.02980.5158-0.0360.0883-0.0227-0.0975-0.0425-0.0189-0.0447-0.02370.00980.06570.00530.00430.048-0.01520.05892.0801-15.7371-36.1339
60.4717-0.21960.07810.498-0.06690.2657-0.00980.0075-0.0474-0.02270.0224-0.00420.03840.0116-0.01020.0548-0.00550.00020.0537-0.00370.05851.2358-16.1484-27.166
70.5743-0.067-0.17480.71580.11010.6802-0.00830.0604-0.0207-0.09680.00040.07790.0227-0.07790.0080.0546-0.0042-0.01830.0601-0.00310.0618-16.4896-0.4298-36.726
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 297:402)A297 - 402

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