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- PDB-1o9t: Methionine adenosyltransferase complexed with both substrates ATP... -

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Basic information

Entry
Database: PDB / ID: 1o9t
TitleMethionine adenosyltransferase complexed with both substrates ATP and methionine
ComponentsS-ADENOSYLMETHIONINE SYNTHETASE
KeywordsTRANSFERASE / ADENOSYLTRANSFERASE / ATP BINDING / METHIONINE BINDING / ONE-CARBON METABOLISM / MAGNESIUM / POTASSIUM / METAL-BINDING / MULTIGENE FAMILY / ATP-BINDING
Function / homology
Function and homology information


Metabolism of ingested SeMet, Sec, MeSec into H2Se / Sulfur amino acid metabolism / L-methionine catabolic process / methionine adenosyltransferase complex / Methylation / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / amino acid binding / one-carbon metabolic process ...Metabolism of ingested SeMet, Sec, MeSec into H2Se / Sulfur amino acid metabolism / L-methionine catabolic process / methionine adenosyltransferase complex / Methylation / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / amino acid binding / one-carbon metabolic process / ADP binding / nuclear matrix / protein-containing complex assembly / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
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 ...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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / METHIONINE / PHOSPHATE ION / S-adenosylmethionine synthase isoform type-1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGonzalez, B. / Pajares, M.A. / Hermoso, J.A. / Sanz-Aparicio, J.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Crystal Structures of Methionine Adenosyltransferase Complexed with Substrates and Products Reveal the Methionine-ATP Recognition and Give Insights Into the Catalytic Mechanism
Authors: Gonzalez, B. / Pajares, M.A. / Hermoso, J.A. / Guillerm, D. / Guillerm, G. / Sanz-Aparicio, J.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: The Crystal Structure of Tetrameric Methionine Adenosyltransferase Fom Rat Liver Reveals the Methionine Binding Site
Authors: Gonzalez, B. / Pajares, M.A. / Hermoso, J.A. / Alvarez, L. / Garrido, F. / Sufrin, J.R. / Sanz-Aparicio, J.
History
DepositionDec 18, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-ADENOSYLMETHIONINE SYNTHETASE
B: S-ADENOSYLMETHIONINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,27311
Polymers87,2752
Non-polymers9979
Water3,171176
1
A: S-ADENOSYLMETHIONINE SYNTHETASE
B: S-ADENOSYLMETHIONINE SYNTHETASE
hetero molecules

A: S-ADENOSYLMETHIONINE SYNTHETASE
B: S-ADENOSYLMETHIONINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,54622
Polymers174,5514
Non-polymers1,99518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+3/41
MethodPQS
Unit cell
Length a, b, c (Å)114.990, 114.990, 160.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7849, -0.2307, 0.575), (-0.218, -0.7659, -0.6049), (0.58, -0.6001, 0.5509)
Vector: 11.2421, 81.4903, 27.3966)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein S-ADENOSYLMETHIONINE SYNTHETASE / METHIONINE ADENOSYLTRANSFERASE / ADOMET SYNTHETASE / MAT-I


Mass: 43637.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: LIVER / Plasmid: PSSRL-T7N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13444, methionine adenosyltransferase

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Non-polymers , 6 types, 185 molecules

#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYSES THE REACTION BETWEEN ATP AND L-METHIONINE, RESULTING IN THE FORMATION OF S-ADENOSYLMETHIONINE
Sequence detailsTHE SWISS-PROT ACCESSION FOR THIS ENTRY P13444 HAS A RESIDUE ASN AT POSITION 345. THE DEPOSITORS ...THE SWISS-PROT ACCESSION FOR THIS ENTRY P13444 HAS A RESIDUE ASN AT POSITION 345. THE DEPOSITORS INDICATE THAT THIS IS A POSSIBLE ERROR IN THE SWISS-PROT DATABASE ENTRY FOR THIS PROTEIN, AND THAT RESIDUE 345 ASN DOES DOES NOT EXIST IN THE STRUCTURE WHICH IS DESCRIBED HERE. THE DBREF CONSEQUENTLY MAPS TO THE SWISS-PROT ENTRY IN TWO PARTS AS SHOWN BELOW.

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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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growpH: 7.5
Details: 16% PEG 10000, 10MM L-METHIONINE, 100MM HEPES PH=7.5 (SOAKING IN 30 MM ATP SOLUTION), pH 7.50
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
250 mMTris-HCl1droppH8.
310 mMdithiothreitol1drop
450 mM1dropKCl
510 mM1dropMgSO4
61 mMEDTA1drop
716 %(w/v)PEG100001reservoir
8100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.76→44.7 Å / Num. obs: 27747 / % possible obs: 97.5 % / Observed criterion σ(I): 4 / Redundancy: 4.1 % / Rsym value: 0.074 / Net I/σ(I): 7.7
Reflection shellResolution: 2.76→2.92 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.443 / % possible all: 97.9
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 27790 / Redundancy: 4.1 % / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.82 Å / % possible obs: 97.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QM4

1qm4


Resolution: 2.9→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1446 7.2 %RANDOM
Rwork0.265 ---
obs0.265 20154 93.5 %-
Displacement parametersBiso mean: 37.4 Å2
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5692 0 55 176 5923
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.16
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.9→3.02 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.348 159 6.6 %
Rwork0.36 2252 -
obs--90.8 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 25 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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