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- PDB-8ovh: Crystal structure of O-acetyl-L-homoserine sulfhydrolase from Sac... -

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Basic information

Entry
Database: PDB / ID: 8ovh
TitleCrystal structure of O-acetyl-L-homoserine sulfhydrolase from Saccharomyces cerevisiae in complex with Pyridoxal-5'-phosphate
ComponentsHomocysteine/cysteine synthase
KeywordsLYASE / Homocysteine/cysteine synthase / O-acetyl-L-homoserine lyase
Function / homology
Function and homology information


O-acetylhomoserine aminocarboxypropyltransferase / O-acetylhomoserine sulfhydrylase activity / O-acetylhomoserine aminocarboxypropyltransferase activity / methionine metabolic process / L-homocysteine biosynthetic process / cysteine synthase / sulfate assimilation / cysteine biosynthetic process / cysteine synthase activity / transsulfuration ...O-acetylhomoserine aminocarboxypropyltransferase / O-acetylhomoserine sulfhydrylase activity / O-acetylhomoserine aminocarboxypropyltransferase activity / methionine metabolic process / L-homocysteine biosynthetic process / cysteine synthase / sulfate assimilation / cysteine biosynthetic process / cysteine synthase activity / transsulfuration / cysteine biosynthetic process from serine / pyridoxal phosphate binding / plasma membrane / cytoplasm
Similarity search - Function
O-acetylhomoserine/O-acetylserine sulfhydrylase / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Homocysteine/cysteine synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.171 Å
AuthorsSaleem-Batcha, R. / Andexer, J.N. / Mohr, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC project 716966European Union
Citation
Journal: Chemistry / Year: 2023
Title: Enzymatic Synthesis of l-Methionine Analogues and Application in a Methyltransferase Catalysed Alkylation Cascade.
Authors: Mohr, M.K.F. / Saleem-Batcha, R. / Cornelissen, N.V. / Andexer, J.N.
#1: Journal: Chemistry / Year: 2023
Title: Enzymatic Synthesis of l-Methionine Analogues and Application in a Methyltransferase Catalysed Alkylation Cascade.
Authors: Mohr, M.K.F. / Saleem-Batcha, R. / Cornelissen, N.V. / Andexer, J.N.
History
DepositionApr 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Sep 18, 2024Group: Database references / Category: citation / citation_author
Revision 1.3Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homocysteine/cysteine synthase
B: Homocysteine/cysteine synthase
C: Homocysteine/cysteine synthase
D: Homocysteine/cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,00412
Polymers203,5914
Non-polymers1,4138
Water8,683482
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19050 Å2
ΔGint-79 kcal/mol
Surface area52570 Å2
Unit cell
Length a, b, c (Å)61.579, 118.218, 131.381
Angle α, β, γ (deg.)90.000, 92.908, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Homocysteine/cysteine synthase / O-acetylserine/O-acetylhomoserine sulfhydrylase / OAS-OAH SHLase / OAS-OAH sulfhydrylase


Mass: 50897.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MET17, MET15, MET25, YLR303W, L8003.1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06106, cysteine synthase, O-acetylhomoserine aminocarboxypropyltransferase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.13 % / Description: Yellow Cuboid blocks
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 22% (w/v) PEG 6000, 200 mM LiCl, and 100 mM sodium acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→49.59 Å / Num. obs: 629183 / % possible obs: 97.46 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.7
Reflection shellResolution: 2.17→2.21 Å / Rmerge(I) obs: 1.6 / Num. unique obs: 3958

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.171→49.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.644 / SU ML: 0.161 / Cross valid method: FREE R-VALUE / ESU R: 0.217 / ESU R Free: 0.199
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2376 4833 5 %
Rwork0.1715 91819 -
all0.175 --
obs-96652 97.447 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.594 Å2
Baniso -1Baniso -2Baniso -3
1--0.078 Å20 Å20.034 Å2
2---0.051 Å20 Å2
3---0.125 Å2
Refinement stepCycle: LAST / Resolution: 2.171→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12380 0 88 482 12950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212785
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611815
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.64717364
X-RAY DIFFRACTIONr_angle_other_deg0.5161.57127232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64351586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.834540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.562101968
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.86610580
X-RAY DIFFRACTIONr_chiral_restr0.0750.21888
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214846
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022930
X-RAY DIFFRACTIONr_nbd_refined0.220.22738
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.211454
X-RAY DIFFRACTIONr_nbtor_refined0.1880.26345
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.26939
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2543
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3290.211
X-RAY DIFFRACTIONr_nbd_other0.2210.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.070.25
X-RAY DIFFRACTIONr_mcbond_it5.2245.1936389
X-RAY DIFFRACTIONr_mcbond_other5.225.1936389
X-RAY DIFFRACTIONr_mcangle_it7.3429.2977960
X-RAY DIFFRACTIONr_mcangle_other7.3439.2997961
X-RAY DIFFRACTIONr_scbond_it6.0725.8066396
X-RAY DIFFRACTIONr_scbond_other6.0715.8056397
X-RAY DIFFRACTIONr_scangle_it8.85210.4169404
X-RAY DIFFRACTIONr_scangle_other8.85210.4169405
X-RAY DIFFRACTIONr_lrange_it11.25749.66214408
X-RAY DIFFRACTIONr_lrange_other11.26349.60314344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.171-2.2270.3563050.3195798X-RAY DIFFRACTION83.1811
2.227-2.2880.3173310.2866286X-RAY DIFFRACTION93.1841
2.288-2.3540.2823400.236461X-RAY DIFFRACTION98.6796
2.354-2.4260.2683340.2076353X-RAY DIFFRACTION99.4349
2.426-2.5060.2783250.2036167X-RAY DIFFRACTION99.6011
2.506-2.5930.2583130.1915943X-RAY DIFFRACTION99.5228
2.593-2.6910.2453030.1725771X-RAY DIFFRACTION99.7045
2.691-2.80.2482930.1635553X-RAY DIFFRACTION98.9673
2.8-2.9250.2282760.1645237X-RAY DIFFRACTION98.6755
2.925-3.0670.2522640.1685038X-RAY DIFFRACTION98.0762
3.067-3.2320.2532530.1744818X-RAY DIFFRACTION99.5094
3.232-3.4270.2412430.1714605X-RAY DIFFRACTION99.4666
3.427-3.6620.2382240.1644265X-RAY DIFFRACTION99.2263
3.662-3.9540.1862110.1394003X-RAY DIFFRACTION99.2697
3.954-4.3290.2041900.1313608X-RAY DIFFRACTION97.0859
4.329-4.8350.2041760.1343344X-RAY DIFFRACTION99.127
4.835-5.5740.1921570.1482989X-RAY DIFFRACTION99.4625
5.574-6.8060.2551330.1842524X-RAY DIFFRACTION99.4014
6.806-9.5350.2161010.1521902X-RAY DIFFRACTION96.9506
9.535-49.590.301610.2341154X-RAY DIFFRACTION99.7537

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