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- PDB-7kb0: O-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Th... -

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Basic information

Entry
Database: PDB / ID: 7kb0
TitleO-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Thermotoga maritima with pyridoxal-5-phosphate (PLP) bound in the internal aldimine state
ComponentsO-acetyl-L-homoserine sulfhydrylase
KeywordsTRANSFERASE / Thermotoga maritima / methionine biosynthesis / enzyme kinetics / O-acety-L-homoserine aminocarboxypropyltransferase / MetY / active site
Function / homology
Function and homology information


O-acetylhomoserine sulfhydrylase activity / L-homocysteine biosynthetic process / cysteine synthase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / transsulfuration / pyridoxal phosphate binding
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
O-acetyl-L-homoserine sulfhydrylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBrewster, J.L. / Pachl, P. / Squire, C. / Selmer, M. / Patrick, W.M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund New Zealand
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structures and kinetics of Thermotoga maritima MetY reveal new insights into the predominant sulfurylation enzyme of bacterial methionine biosynthesis.
Authors: Brewster, J.L. / Pachl, P. / McKellar, J.L.O. / Selmer, M. / Squire, C.J. / Patrick, W.M.
History
DepositionOct 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-acetyl-L-homoserine sulfhydrylase


Theoretical massNumber of molelcules
Total (without water)47,3141
Polymers47,3141
Non-polymers00
Water3,189177
1
A: O-acetyl-L-homoserine sulfhydrylase

A: O-acetyl-L-homoserine sulfhydrylase

A: O-acetyl-L-homoserine sulfhydrylase

A: O-acetyl-L-homoserine sulfhydrylase


Theoretical massNumber of molelcules
Total (without water)189,2584
Polymers189,2584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area21350 Å2
ΔGint-91 kcal/mol
Surface area47260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.308, 135.308, 110.878
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-587-

HOH

21A-596-

HOH

31A-671-

HOH

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Components

#1: Protein O-acetyl-L-homoserine sulfhydrylase / OAH sulfhydrylase / O-acetylhomoserine thiolase


Mass: 47314.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0882, Tmari_0884 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZY4, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.4
Details: 0.1 M BIS-Tris, 0.2 M magnesium chloride, 18% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→42.88 Å / Num. obs: 51081 / % possible obs: 99.4 % / Redundancy: 7.62 % / Biso Wilson estimate: 24.25 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.246 / Net I/σ(I): 7.13
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 7.75 % / Num. unique obs: 8154 / CC1/2: 0.302 / Rrim(I) all: 1.869 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PHENIXphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T. maritima CBL

Resolution: 1.85→42.88 Å / SU ML: 0.2886 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 2590 5.07 %
Rwork0.2097 48490 -
obs0.2115 51080 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.71 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 0 177 3452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01433349
X-RAY DIFFRACTIONf_angle_d1.24364558
X-RAY DIFFRACTIONf_chiral_restr0.0697518
X-RAY DIFFRACTIONf_plane_restr0.0105588
X-RAY DIFFRACTIONf_dihedral_angle_d16.58371193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.40911180.37292523X-RAY DIFFRACTION98.99
1.88-1.920.36361310.34842529X-RAY DIFFRACTION99.92
1.92-1.960.35141380.31062506X-RAY DIFFRACTION99.96
1.96-20.28431200.3022539X-RAY DIFFRACTION99.92
2-2.050.34761320.29332518X-RAY DIFFRACTION99.96
2.05-2.10.34311310.28752538X-RAY DIFFRACTION99.89
2.1-2.160.31671390.26662531X-RAY DIFFRACTION99.85
2.16-2.220.26171550.26032527X-RAY DIFFRACTION99.85
2.22-2.290.271310.25262524X-RAY DIFFRACTION99.92
2.29-2.370.30271610.24612524X-RAY DIFFRACTION99.78
2.37-2.470.28671500.2392527X-RAY DIFFRACTION99.66
2.47-2.580.26491230.22732548X-RAY DIFFRACTION99.55
2.58-2.720.26071530.21822528X-RAY DIFFRACTION99.41
2.72-2.890.24061100.20122580X-RAY DIFFRACTION99.41
2.89-3.110.271320.20012564X-RAY DIFFRACTION99.34
3.11-3.420.21741240.17632583X-RAY DIFFRACTION99.16
3.42-3.920.18911400.15342577X-RAY DIFFRACTION98.76
3.92-4.940.15191510.13792593X-RAY DIFFRACTION98.14
4.94-42.880.21691510.18322731X-RAY DIFFRACTION97.07
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.65353705315-0.586569131355-0.07612879270060.5922938433480.1329044129380.4664224619060.192222425211-0.1601208614950.079223862617-0.0382796565932-0.080338825588-0.142979089007-0.2507124650840.184202274775-0.08021696711470.156579017144-0.00624046349220.01799699677170.2836423122940.0008064588954490.18245515976151.559366690765.478733210971.019960038
21.4448145506-0.997996420755-0.3204296166780.8663256235320.2341595034270.3871086160280.2931697963670.5625542752130.551936991178-0.193845129341-0.263543881517-0.376991308722-0.2757408878920.0399325533151-0.0383401106770.2010155735730.05160384455740.06749022615390.2758932342480.06674179365530.27235254331342.280551369773.493031046760.3446952292
31.06415810651-0.08970112380580.07394227116650.7213080315080.4528390281261.137893812340.09070783758880.170298979346-0.177401254882-0.0249893697193-0.0145058205474-0.01383064961790.123305740442-0.0392199653215-0.08006132114750.1196300353820.0577692890665-0.006485387653210.2458170774530.001919695862190.15445242727844.869430346750.967897341141.391140838
40.540599054248-0.559085059292-0.05546383144180.918793325065-0.6416470301331.79842808926-0.01744206328470.0381682809430.003669826402360.00904702714010.010293744628-0.1414321326240.05838450991180.24477686927-0.0109491568650.09556477458840.03847782196620.006054743188790.2253827778-0.01606337274780.16710055409355.654499406349.736929241648.6175675617
50.8235145349450.377347325017-0.4855250003931.2431900542-0.8627499781441.820975267860.04941940227140.005065113229720.1205382629730.01263237066170.0752057760096-0.0122985071692-0.1369064469060.106893434883-0.06985137934590.1115607838380.05062139536290.02460460481260.2008268712850.009465524891520.19076950121646.721230453762.280666855448.5930202894
60.1520335695210.0633963577545-0.0002835372204650.840077117858-0.2149376436230.9916064908090.03442786613110.08486542120130.05654481532550.000622379516798-0.0812490695095-0.09931558330880.03820163840540.04129862665280.05498877890140.1190376066690.05909220967840.01177024962390.2131380797410.0007020709029370.16112302080847.726607824754.638084935559.279189768
70.9569430725770.0484555345381-0.8723896783361.17115888816-0.4422893815292.030992725160.1019975561950.246433124892-0.0252138165529-0.163226577307-0.06202002258650.1143365171950.292785261097-0.176684326528-0.03740780285590.2860284089610.0860263654829-0.08312052417920.226750227502-0.04160230038220.22452036419846.826306160532.158867814857.1282746837
80.8721827995660.093872258129-0.4114364734541.43967324496-0.261592966980.9541336881110.01677516060290.2620569978980.00077795582133-0.147669377477-0.009378305407-0.05693715333770.5898072445140.021534673212-0.0240921887490.3872334718810.0587924163304-0.04622638074610.23948429041-0.00434534957940.23509827217144.383593514428.776291347960.0788208532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 157 )
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 207 )
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 250 )
6X-RAY DIFFRACTION6chain 'A' and (resid 251 through 311 )
7X-RAY DIFFRACTION7chain 'A' and (resid 312 through 390 )
8X-RAY DIFFRACTION8chain 'A' and (resid 391 through 429 )

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