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- PDB-8swa: Crystal structure of the human S-adenosylmethionine synthetase 1 ... -

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Basic information

Entry
Database: PDB / ID: 8swa
TitleCrystal structure of the human S-adenosylmethionine synthetase 1 in complex with SAM and PPNP
ComponentsS-adenosylmethionine synthase isoform type-1
KeywordsTRANSFERASE / Complex / 1-carbon / SAM
Function / homology
Function and homology information


Defective MAT1A causes MATD / L-methionine catabolic process / Sulfur amino acid metabolism / methionine adenosyltransferase complex / Metabolism of ingested SeMet, Sec, MeSec into H2Se / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / one-carbon metabolic process ...Defective MAT1A causes MATD / L-methionine catabolic process / Sulfur amino acid metabolism / methionine adenosyltransferase complex / Metabolism of ingested SeMet, Sec, MeSec into H2Se / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / one-carbon metabolic process / protein homotetramerization / ATP binding / metal ion binding / identical protein 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
: / (DIPHOSPHONO)AMINOPHOSPHONIC ACID / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase isoform type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsBruemmer, K.J. / Pham, V.N. / Toh, J.D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Science / Year: 2023
Title: Formaldehyde regulates S -adenosylmethionine biosynthesis and one-carbon metabolism.
Authors: Pham, V.N. / Bruemmer, K.J. / Toh, J.D.W. / Ge, E.J. / Tenney, L. / Ward, C.C. / Dingler, F.A. / Millington, C.L. / Garcia-Prieto, C.A. / Pulos-Holmes, M.C. / Ingolia, N.T. / Pontel, L.B. / ...Authors: Pham, V.N. / Bruemmer, K.J. / Toh, J.D.W. / Ge, E.J. / Tenney, L. / Ward, C.C. / Dingler, F.A. / Millington, C.L. / Garcia-Prieto, C.A. / Pulos-Holmes, M.C. / Ingolia, N.T. / Pontel, L.B. / Esteller, M. / Patel, K.J. / Nomura, D.K. / Chang, C.J.
History
DepositionMay 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylmethionine synthase isoform type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5806
Polymers44,8371
Non-polymers7435
Water4,161231
1
A: S-adenosylmethionine synthase isoform type-1
hetero molecules

A: S-adenosylmethionine synthase isoform type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,16012
Polymers89,6742
Non-polymers1,48610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8060 Å2
ΔGint-73 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.698, 100.421, 122.740
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-735-

HOH

21A-783-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein S-adenosylmethionine synthase isoform type-1 / AdoMet synthase 1 / Methionine adenosyltransferase 1 / MAT 1 / Methionine adenosyltransferase I/III ...AdoMet synthase 1 / Methionine adenosyltransferase 1 / MAT 1 / Methionine adenosyltransferase I/III / MAT-I/III


Mass: 44837.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT1A, AMS1, MATA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q00266, methionine adenosyltransferase

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Non-polymers , 5 types, 236 molecules

#2: Chemical ChemComp-PPK / (DIPHOSPHONO)AMINOPHOSPHONIC ACID


Mass: 256.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H6NO9P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: human N16-MAT1A protein (6 mg/mL), 1 mM MgCl2, 5 mM KCl, 1 mM adenylyl-imidodiphosphate (AMP-PNP) and 1 mM L-Methionine was mixed with 60 to 75% 2-methyl-2,4-pentadiol (MPD) diluted with 100 ...Details: human N16-MAT1A protein (6 mg/mL), 1 mM MgCl2, 5 mM KCl, 1 mM adenylyl-imidodiphosphate (AMP-PNP) and 1 mM L-Methionine was mixed with 60 to 75% 2-methyl-2,4-pentadiol (MPD) diluted with 100 mM HEPES pH 7-8 (Hampton) in 2:1 or 1:1 volume ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. obs: 26118 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.057 / Rrim(I) all: 0.214 / Χ2: 2.012 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0311.50.80113130.9150.2420.8380.549100
2.03-2.0712.30.80312620.910.2310.8361.47899.8
2.07-2.1112.80.73412840.9290.210.7640.69100
2.11-2.1513.60.64212770.9580.1780.6670.62699.8
2.15-2.214.10.58312980.9520.1590.6040.76799.9
2.2-2.2514.60.56213020.9680.1520.5821.301100
2.25-2.3114.60.4712920.9730.1270.4870.795100
2.31-2.3714.60.42112810.9730.1130.4370.833100
2.37-2.4414.70.3612940.9780.0960.3720.881100
2.44-2.5214.60.35412850.9760.0950.3671.071100
2.52-2.6114.70.28912880.9760.0780.2990.978100
2.61-2.7114.70.24213120.9880.0650.2511.26100
2.71-2.8414.60.20513110.9890.0550.2121.36100
2.84-2.9914.60.17812900.9910.0480.1851.679100
2.99-3.1714.60.15913060.9910.0430.1652.241100
3.17-3.4214.50.14413130.9920.0390.153.417100
3.42-3.7614.40.12513080.9950.0340.1294.355100
3.76-4.3114.10.10913330.9970.0310.1135.133100
4.31-5.4314.30.08113510.9970.0220.0844.229100
5.43-5013.70.06414180.9960.0180.0675.736100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3211refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2obv

2obv


Resolution: 1.999→38.861 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1938 1999 7.66 %
Rwork0.1434 24114 -
obs0.1472 26113 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.58 Å2 / Biso mean: 18.1958 Å2 / Biso min: 5.55 Å2
Refinement stepCycle: final / Resolution: 1.999→38.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 43 231 3206
Biso mean--18.69 27.52 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073060
X-RAY DIFFRACTIONf_angle_d0.9334162
X-RAY DIFFRACTIONf_dihedral_angle_d8.5522514
X-RAY DIFFRACTIONf_chiral_restr0.058470
X-RAY DIFFRACTIONf_plane_restr0.006534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.999-2.0490.2321330.1694160495
2.049-2.10440.2191410.14991707100
2.1044-2.16630.19741400.14651685100
2.1663-2.23620.17721430.1431724100
2.2362-2.31610.2281420.13741705100
2.3161-2.40890.19551420.13951723100
2.4089-2.51850.19871420.14731697100
2.5185-2.65120.18371430.14461735100
2.6512-2.81730.19961420.14441706100
2.8173-3.03470.20861440.14271740100
3.0347-3.340.18791430.13951725100
3.34-3.82290.16571450.13121747100
3.8229-4.81510.19771450.13021769100
4.8151-38.860.18091540.16361847100

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