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- PDB-3vk4: Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas pu... -

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Basic information

Entry
Database: PDB / ID: 3vk4
TitleCrystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant complexed with L-homocysteine
ComponentsMethionine gamma-lyase
KeywordsLYASE / PLP-dependent enzyme / PLP
Function / homology
Function and homology information


homocysteine desulfhydrase / homocysteine desulfhydrase activity / methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
L-methionine gamma-lyase / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...L-methionine gamma-lyase / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-methionine gamma-lyase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsFukumoto, M. / Kudou, D. / Murano, S. / Shiba, T. / Sato, D. / Tamura, T. / Harada, S. / Inagaki, K.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2012
Title: The role of amino acid residues in the active site of L-methionine gamma-lyase from Pseudomonas putida.
Authors: Fukumoto, M. / Kudou, D. / Murano, S. / Shiba, T. / Sato, D. / Tamura, T. / Harada, S. / Inagaki, K.
History
DepositionNov 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _citation.title ..._citation.pdbx_database_id_DOI / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Mar 6, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine gamma-lyase
B: Methionine gamma-lyase
C: Methionine gamma-lyase
D: Methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,2888
Polymers171,7474
Non-polymers5414
Water1,42379
1
A: Methionine gamma-lyase
B: Methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1444
Polymers85,8732
Non-polymers2702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-27 kcal/mol
Surface area28300 Å2
MethodPISA
2
C: Methionine gamma-lyase
D: Methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1444
Polymers85,8732
Non-polymers2702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-22 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.488, 153.487, 80.671
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Methionine gamma-lyase / L-methioninase


Mass: 42936.738 Da / Num. of mol.: 4 / Mutation: C116H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdeA / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P13254, methionine gamma-lyase
#2: Chemical
ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9NO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 12.5% PEG6000, 0.25M ammonium sulfate, 0.2M MES, 0.5mM PLP, 0.5% 2-mercaptoethanol, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 17, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 57780 / Num. obs: 57379 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.149 / Rsym value: 0.067
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O7C

2o7c


Resolution: 2.61→29.28 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / SU B: 10.481 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.695 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25329 2902 5.1 %RANDOM
Rwork0.19076 ---
all0.19395 57379 --
obs0.19395 54542 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.487 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.61→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11907 0 32 79 12018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02112199
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.96816571
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53251568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21723.346517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.1151878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4931580
X-RAY DIFFRACTIONr_chiral_restr0.1190.21859
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219340
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.861.57799
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.634212401
X-RAY DIFFRACTIONr_scbond_it2.24434400
X-RAY DIFFRACTIONr_scangle_it3.6694.54170
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.613→2.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 180 -
Rwork0.241 3610 -
obs--89.26 %

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