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- PDB-1qm4: Methionine Adenosyltransferase Complexed with a L-Methionine Analogue -

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Basic information

Entry
Database: PDB / ID: 1qm4
TitleMethionine Adenosyltransferase Complexed with a L-Methionine Analogue
ComponentsMETHIONINE ADENOSYLTRANSFERASE, ALPHA FORMS-Adenosylmethionine synthetase enzyme
KeywordsTRANSFERASE / ADENOSYLTRANSFERASE / METHIONINE BINDING
Function / homology
Function and homology information


Metabolism of ingested SeMet, Sec, MeSec into H2Se / Sulfur amino acid metabolism / methionine catabolic process / methionine adenosyltransferase complex / Methylation / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / amino acid binding / ADP binding ...Metabolism of ingested SeMet, Sec, MeSec into H2Se / Sulfur amino acid metabolism / methionine catabolic process / methionine adenosyltransferase complex / Methylation / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / amino acid binding / ADP binding / nuclear matrix / one-carbon metabolic process / protein homotetramerization / protein-containing complex assembly / 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
L-2-AMINO-4-METHOXY-CIS-BUT-3-ENOIC ACID / : / S-adenosylmethionine synthase isoform type-1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsGonzalez, B. / Pajares, M.A. / Hermoso, J.A. / Sanz-Aparicio, J.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The Crystal Structure of Tetrameric Methionine Adenosyltransferase from 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.
#1: Journal: Biochem.J. / Year: 1994
Title: Expression of Rat Liver S-Adenosylmethionine Synthetase in Escherichia Coli Results in Two Active Oligomeric Forms
Authors: Alvarez, L. / Mingorance, J. / Pajares, M.A. / Mato, J.M.
History
DepositionSep 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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 / _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_conn.ptnr2_label_seq_id
Revision 1.4May 30, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
B: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,86111
Polymers87,2752
Non-polymers5859
Water3,549197
1
A: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
B: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
hetero molecules

A: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
B: METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,72122
Polymers174,5514
Non-polymers1,17018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+3/41
Buried area12050 Å2
ΔGint-82.7 kcal/mol
Surface area61270 Å2
MethodPQS
Unit cell
Length a, b, c (Å)115.200, 115.200, 159.980
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: (-0.78343, -0.23114, 0.5769), (-0.21651, -0.76861, -0.60197), (0.58255, -0.59651, 0.5521)
Vector: 0.0983, 0.70748, 0.16955)
DetailsTHE ENZYME IS A TETRAMERTHE DIMER IN THE ASYMMETRIC UNIT HAS A PROTEIN PROTEININTERACTION ABOUT THE LARGEST FACE OF THE MONOMERICMOLECULE AND THE TETRAMER IS MADE UP OF TWO OF THESEDIMERS INTERACTING IN A 'HEAD-TO-HEAD' MANNER .IN THE CRYSTAL THE DIMER MOLECULES ARE INVOLVED IN A STRONGCRYSTAL PACKING INTERACTION INVOLVING THE OPPOSITE FACEOF THE MOLECULES TO THAT INVOLVED IN THE BIOLOGICAL DIMER.FOR EXAMPLE SYMMETRY OPERATION,BIOMT1 2 1.000000 0.000000 0. 000000 0.00000BIOMT2 2 0.000000 -1.000000 0.000000 115.20000BIOMT3 2 0.000000 0. 000000 -1.000000 79.99000GENERATES A CRYSTAL PACKING TETRAMERIC ASSEMBLY.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM / S-Adenosylmethionine synthetase enzyme / ADOMET SYNTHETASE / MAT-I / S-ADENOSYLMETHIONINE SYNTHETASE


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 , 5 types, 206 molecules

#2: Chemical ChemComp-AMB / L-2-AMINO-4-METHOXY-CIS-BUT-3-ENOIC ACID


Mass: 131.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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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 10K, 10MM CIS-AMB, 0.1 HEPES PH=7.5, pH 7.50
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Details: drop consists of equal amounts of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 mg/mlprotein1drop
250 mMTris-HCl1drop
310 mML-cisAMB1drop
410 mMdithiothreitol1drop
550 mM1dropKCl
610 mM1dropMgSO4
71 mMEDTA1drop
816 %(w/v)PEG100001reservoirprecipitant
9100 mMHEPES1reservoirprecipitant

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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: Feb 15, 1999
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.66→44.7 Å / Num. obs: 28742 / % possible obs: 94.5 % / Observed criterion σ(I): 4 / Redundancy: 7.5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 6.7
Reflection shellResolution: 2.66→2.8 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.37 / % possible all: 85.8
Reflection shell
*PLUS
% possible obs: 85.8 % / Rmerge(I) obs: 0.37

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MXA

1mxa


Resolution: 2.66→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: NO DENSITY FOR RESIDUES A1-A16, AND B1-B16, WAS OBSERVED IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.29 -7 %RANDOM
Rwork0.23 ---
obs0.23 28276 84.3 %-
Displacement parametersBiso mean: 41.5 Å2
Refinement stepCycle: LAST / Resolution: 2.66→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5692 0 29 197 5918
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.03
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: 2.66→2.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.34 -7 %
Rwork0.28 3100 -
obs--70 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTIOH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.03

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