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- PDB-7kb1: Complex of O-acety-L-homoserine aminocarboxypropyltransferase (Me... -

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Basic information

Entry
Database: PDB / ID: 7kb1
TitleComplex of O-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Thermotoga maritima and a key reaction intermediate
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 / transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / methionine biosynthetic process / 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
TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Chem-WBJ / 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 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
B: O-acetyl-L-homoserine sulfhydrylase
C: O-acetyl-L-homoserine sulfhydrylase
D: O-acetyl-L-homoserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,78011
Polymers188,3454
Non-polymers1,4357
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22480 Å2
ΔGint-119 kcal/mol
Surface area46600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.580, 151.340, 91.390
Angle α, β, γ (deg.)90.000, 112.041, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 2 - 429 / Label seq-ID: 2 - 429

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and (resid 2 or (resid 3 through 5...AA
22(chain 'B' and (resid 2 or (resid 3 through 5...BB
33(chain 'C' and (resid 2 through 39 or (resid 40...CC
44(chain 'D' and (resid 2 through 46 or (resid 47...DD

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 47086.266 Da / Num. of mol.: 4
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

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Non-polymers , 6 types, 607 molecules

#2: Chemical ChemComp-WBJ / (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid


Mass: 330.230 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C12H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.4
Details: 0.1 M BIS-Tris, pH 5.4, 0.2 M magnesium chloride, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953729 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953729 Å / Relative weight: 1
ReflectionResolution: 1.85→48.37 Å / Num. obs: 134424 / % possible obs: 92.8 % / Redundancy: 2.49 % / Biso Wilson estimate: 27.99 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.054 / Net I/σ(I): 11.28
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2.28 % / Mean I/σ(I) obs: 1.87 / Num. unique obs: 7815 / CC1/2: 0.781 / Rrim(I) all: 0.53 / % possible all: 72.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1000251999

Resolution: 1.85→48.37 Å / SU ML: 0.3088 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.5234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2619 6825 5.08 %
Rwork0.2267 127591 -
obs0.2285 134416 92.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.9 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12947 0 92 600 13639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003113331
X-RAY DIFFRACTIONf_angle_d0.595818156
X-RAY DIFFRACTIONf_chiral_restr0.04722072
X-RAY DIFFRACTIONf_plane_restr0.00462338
X-RAY DIFFRACTIONf_dihedral_angle_d16.48614692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.35931660.34243112X-RAY DIFFRACTION67.64
1.87-1.890.36791730.32643471X-RAY DIFFRACTION75.76
1.89-1.920.4081570.34693918X-RAY DIFFRACTION84.77
1.92-1.940.37972080.33544036X-RAY DIFFRACTION87.67
1.94-1.970.40432240.33834158X-RAY DIFFRACTION92.04
1.97-1.990.36272610.33444342X-RAY DIFFRACTION95.32
1.99-2.020.37632290.33514380X-RAY DIFFRACTION96.08
2.02-2.050.33512450.31814416X-RAY DIFFRACTION96.5
2.05-2.080.3682330.32744322X-RAY DIFFRACTION95.59
2.08-2.120.39382130.32634445X-RAY DIFFRACTION96.08
2.12-2.150.3572120.3224391X-RAY DIFFRACTION96.34
2.15-2.190.38812120.30934395X-RAY DIFFRACTION96
2.19-2.240.32132770.30994359X-RAY DIFFRACTION95.67
2.24-2.280.37252700.30884340X-RAY DIFFRACTION96.04
2.28-2.330.35052240.2924449X-RAY DIFFRACTION95.92
2.33-2.380.33692350.29364313X-RAY DIFFRACTION95.59
2.38-2.440.34462000.27824383X-RAY DIFFRACTION95
2.44-2.510.29132270.27164274X-RAY DIFFRACTION93.73
2.51-2.580.30312490.27084359X-RAY DIFFRACTION95.78
2.58-2.670.36092300.2654432X-RAY DIFFRACTION96.76
2.67-2.760.28362360.25054406X-RAY DIFFRACTION96.11
2.76-2.870.2842450.2444407X-RAY DIFFRACTION96.61
2.87-30.28792430.23864415X-RAY DIFFRACTION96.82
3-3.160.30682390.23994406X-RAY DIFFRACTION95.83
3.16-3.360.23642480.20634330X-RAY DIFFRACTION94.96
3.36-3.620.22972340.1974244X-RAY DIFFRACTION93.02
3.62-3.980.1932140.17014316X-RAY DIFFRACTION93.4
3.99-4.560.19062300.14844335X-RAY DIFFRACTION93.97
4.56-5.750.16272700.14434233X-RAY DIFFRACTION92.75
5.75-48.370.15712210.15164204X-RAY DIFFRACTION90.36
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)
10.485315819276-0.1277286113090.2625697511980.0344364959861-0.06953989673730.146873813868-0.0205153760316-0.254633685697-0.0744816899976-0.07851489447440.02757170461350.0946529115508-0.0115950788169-0.1015778884840.004587834436350.2010903734840.0106322635111-0.02380448258390.140356382549-0.02408712452180.229090678122-7.52528615217-8.550398649317.5489451317
20.0203707440313-0.002788716691336.81997840452E-50.02072319735980.0008930956119630.008074732718770.0125048663443-0.01822648720780.0434968749428-0.167336405586-0.00169199079090.120227131041-0.0782867325011-0.04179163030510.1205572182110.2969910205790.0302287634547-0.0242134571951-0.11877364653-0.04881655874340.09380662845291.77024509777-4.439815769112.16939528376
30.0192311117146-0.0243608174371-0.004575031449340.09395916935910.00746423009210.00105025773481-0.0500331578295-0.03389234955190.0565273606892-0.0432809411063-0.003717637140880.0293198718365-0.07049509599710.00741798753959-0.1129922736680.294496620266-0.05523898666610.01893856527490.0745788730695-0.1404862880290.26510845820818.210909422114.1056678839.61103587951
40.0664814831346-0.0344116995785-0.0432763469320.02346710888090.01187308826830.0677799800096-0.0198667706548-0.1657149075280.143649218629-0.117807456436-0.0138064395555-0.04204985513240.02452645278660.0170936046614-0.04644296784610.247714350447-0.04764244442290.02305365479430.199600235889-0.08085496950680.21668745148825.958836765.1719997822412.9315234031
50.00500727423904-0.00698078756867-0.00814454037590.03406033363930.0336947875020.0357990564209-0.0243211703698-0.209427713302-0.108731119614-0.04126014457840.0547111702049-0.0422514242753-0.04351660103020.03608024635260.003397064392530.1697493527140.0168952879190.01293244160020.4138234657320.1068721765160.23674839603823.8627099193-17.818461500625.8211334435
60.120222180290.00446197401127-0.01669273272030.00576271086483-0.003734739526720.00200041651718-0.0697080633787-0.184450500656-0.336366668663-0.0994820175234-0.00272186046358-0.0001334947438440.00692691081110.0367145628268-0.1844857127270.210552410920.0008580108909740.0307384066084-0.159263997740.2832684568850.2962503273711.5182994832-30.00018069419.67000608151
7-0.002896705304910.00434553388622-0.00107441662990.02169489132260.01211004034570.0132035399749-0.089945069132-0.0578682930931-0.146099776317-0.0121341897784-0.02761518465530.0001489435050260.1202619778174.48801908063E-5-0.2578528771890.18466520732-0.06601397082110.09429313620560.2711716686920.3195018455250.436009222026-4.16901937551-40.699090595425.1567201658
80.01898068453420.01427857421680.01145367442720.107807959494-0.0133067204920.0529370878821-0.0459070153114-0.0621470130365-0.0781258670901-0.03986140251214.64216901347E-50.0712096159010.0627677614184-0.0375900289678-0.1099379175260.262173802798-0.08268780558580.06068776055760.3141124098340.232225569390.544698206569-13.7630340456-34.33369723.0146192543
90.1273639874190.00890485719401-0.005137683802670.0180104162315-0.03613343036970.150540997327-0.0562036290067-0.236617272364-0.01269615267950.05073681856790.0159163971444-0.0377083461244-0.033388162710.0923794217689-0.02231972577570.159383290386-0.000461868296274-0.04718755779380.617102820574-0.006619883288870.16534255762123.1286463839-5.520827713939.3141027297
100.007919755222760.01986064620960.01224321107430.09261564128-0.005798750797530.0615364710179-0.00260660085441-0.375541511370.1569204454810.1574304297070.01536548057190.00921892167762-0.05701773789990.03695649406910.07488974716830.2644336447980.0196369210883-0.05600712409141.11738356083-0.4122693841370.12540561850410.77031903118.1201167277253.9325500169
110.0583741891691-0.0471556108056-0.03831258501350.03116305009110.03052020390840.02659408946910.0242847471389-0.107405802250.0868760489722-0.003999807241860.001446420382260.0185877864001-0.04260346370080.02075814468330.1345216748850.1986485448370.03619714690180.04090964067440.53573463494-0.4105026610870.326295297021-6.6040930863816.543975686638.2953137298
120.0101171142021-0.00166138880289-0.01129508251340.002369128038740.002284414694550.0117208274732-0.00336693374287-0.09628898522650.03749385722280.07015518975470.004402965403740.0468281815060.00226701983668-0.009066519391120.01967741187610.2451805726040.05786491625030.03617189926840.529771516867-0.2973439425460.396396201157-14.419827427415.398270398440.4156260103
130.01486014104820.003479905269810.01633536254560.001053006649040.004264440590740.0214831427115-0.0259580163108-0.0506781251073-0.05871409538380.0225518737652-0.02153133442690.02285978639230.0282083637485-0.0022620441876-0.03627060740010.139602133185-0.02556323177020.07220444654010.4696565032410.1602999522690.311855678208-8.70555794047-21.2011857137.5300788501
140.0485340222945-0.0570792477085-0.03330253637520.1165203703460.1040665491530.117865908213-0.0727708537568-0.315581808935-0.09555596440570.156806625512-0.04281297775150.01070000531220.1140487031140.0863590460993-0.2887928790160.1948183760090.05634428272140.09897149194931.019493103720.203256854190.1017972214761.07289060872-17.333536325859.1533238205
150.03050654952190.03171813596670.03161468768580.112063545439-0.02305255545440.0787018716183-0.0402213982748-0.385987247934-0.127949109120.153402695108-0.126512194547-0.07988782813280.09791192223690.0616438926654-0.5695819007760.2584117774570.07905268613560.04148024374061.056516327730.43507466990.16216172497911.4391067562-24.583416851453.5210119743
160.000432077728915-5.06207772019E-80.0001115520095768.85879856095E-5-0.0003814546422470.0005581809696360.00629585377019-0.00221381294915-0.001556990154170.0008752902284340.0112577826805-0.00292404561113-0.004448949519470.000133411307579-6.96662888235E-50.35783906850.06869061432570.001272597909310.4823175103740.1724811309960.42399064108737.7614414017-34.404379027148.1565480963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:104)
2X-RAY DIFFRACTION2(chain A and resid 105:288)
3X-RAY DIFFRACTION3(chain A and resid 289:356)
4X-RAY DIFFRACTION4(chain A and resid 357:429)
5X-RAY DIFFRACTION5(chain B and resid 2:53)
6X-RAY DIFFRACTION6(chain B and resid 54:278)
7X-RAY DIFFRACTION7(chain B and resid 279:356)
8X-RAY DIFFRACTION8(chain B and resid 357:429)
9X-RAY DIFFRACTION9(chain C and resid 2:61)
10X-RAY DIFFRACTION10(chain C and resid 62:281)
11X-RAY DIFFRACTION11(chain C and resid 282:387)
12X-RAY DIFFRACTION12(chain C and resid 388:429)
13X-RAY DIFFRACTION13(chain D and resid 2:35)
14X-RAY DIFFRACTION14(chain D and resid 36:214)
15X-RAY DIFFRACTION15(chain D and resid 215:422)
16X-RAY DIFFRACTION16(chain D and resid 423:429)

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