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- PDB-6r2c: Crystal structure of the SucA domain of Mycobacterium smegmatis K... -

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Basic information

Entry
Database: PDB / ID: 6r2c
TitleCrystal structure of the SucA domain of Mycobacterium smegmatis KGD after soaking with succinylphosphonate phosphonoethyl ester (PESP)
ComponentsMultifunctional 2-oxoglutarate metabolism enzyme
KeywordsOXIDOREDUCTASE / oxoglutarate dehydrogenase / TPP-dependent decarboxylase
Function / homology
Function and homology information


2-hydroxy-3-oxoadipate synthase / 2-oxoglutarate decarboxylase / 2-oxoglutarate decarboxylase activity / 2-hydroxy-3-oxoadipate synthase activity / oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding ...2-hydroxy-3-oxoadipate synthase / 2-oxoglutarate decarboxylase / 2-oxoglutarate decarboxylase activity / 2-hydroxy-3-oxoadipate synthase activity / oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding / tricarboxylic acid cycle / magnesium ion binding / cytosol
Similarity search - Function
TPP helical domain / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain / Rossmann fold - #12470 / 2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component ...TPP helical domain / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain / Rossmann fold - #12470 / 2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component / Dehydrogenase E1 component / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Chloramphenicol acetyltransferase-like domain superfamily / Thiamin diphosphate-binding fold / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-JQ5 / THIAMINE DIPHOSPHATE / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.09 Å
AuthorsWagner, T. / Alzari, P.M. / Bellinzoni, M.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts.
Authors: Wagner, T. / Boyko, A. / Alzari, P.M. / Bunik, V.I. / Bellinzoni, M.
History
DepositionMar 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multifunctional 2-oxoglutarate metabolism enzyme
B: Multifunctional 2-oxoglutarate metabolism enzyme
C: Multifunctional 2-oxoglutarate metabolism enzyme
D: Multifunctional 2-oxoglutarate metabolism enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,46620
Polymers388,6674
Non-polymers2,79916
Water15,259847
1
A: Multifunctional 2-oxoglutarate metabolism enzyme
B: Multifunctional 2-oxoglutarate metabolism enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,73310
Polymers194,3332
Non-polymers1,4008
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-83 kcal/mol
Surface area55810 Å2
MethodPISA
2
C: Multifunctional 2-oxoglutarate metabolism enzyme
D: Multifunctional 2-oxoglutarate metabolism enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,73310
Polymers194,3332
Non-polymers1,4008
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-81 kcal/mol
Surface area55980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.390, 83.960, 160.680
Angle α, β, γ (deg.)99.54, 98.78, 100.89
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Multifunctional 2-oxoglutarate metabolism enzyme / 2-hydroxy-3-oxoadipate synthase / HOAS / 2-oxoglutarate carboxy-lyase / 2-oxoglutarate ...2-hydroxy-3-oxoadipate synthase / HOAS / 2-oxoglutarate carboxy-lyase / 2-oxoglutarate decarboxylase / Alpha-ketoglutarate decarboxylase / KGD / Alpha-ketoglutarate-glyoxylate carboligase


Mass: 97166.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: kgd, sucA, MSMEG_5049, MSMEI_4922 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0R2B1, 2-hydroxy-3-oxoadipate synthase, 2-oxoglutarate decarboxylase, oxoglutarate dehydrogenase (succinyl-transferring), dihydrolipoyllysine-residue succinyltransferase

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Non-polymers , 5 types, 863 molecules

#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-JQ5 / 4-[ethoxy(oxidanyl)phosphoryl]-4-oxidanylidene-butanoic acid


Mass: 210.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11O6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 60% MPD, 22.5 mM Na acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.09→78.48 Å / Num. obs: 233909 / % possible obs: 97.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 35.94 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.048 / Net I/σ(I): 10
Reflection shellResolution: 2.09→2.12 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 11533 / CC1/2: 0.83 / Rpim(I) all: 0.399 / % possible all: 96.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2YIC

2yic


Resolution: 2.09→21.07 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.211 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.174
RfactorNum. reflection% reflectionSelection details
Rfree0.246 11680 5.01 %RANDOM
Rwork0.232 ---
obs0.233 233039 97.4 %-
Displacement parametersBiso mean: 43.36 Å2
Baniso -1Baniso -2Baniso -3
1--10.374 Å2-3.3678 Å20.4197 Å2
2--3.3983 Å20.0538 Å2
3---6.9756 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.09→21.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25237 0 164 847 26248
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00925925HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9435175HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11959SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes661HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3897HARMONIC5
X-RAY DIFFRACTIONt_it25925HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion2.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3348SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact30900SEMIHARMONIC4
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2594 850 4.96 %
Rwork0.2344 16287 -
all0.2357 17137 -
obs--96.5 %
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)
10.6455-0.16090.09411.0575-0.21280.8181-0.02720.06540.13950.07010.06360.3475-0.0705-0.0769-0.0364-0.06250.0135-0.0172-0.1797-0.01330.0487-17.046615.0785-46.471
20.5494-0.17260.12870.8018-0.22440.7404-0.0747-0.1307-0.09020.36750.07630.10430.17050.1122-0.00170.17260.09320.0322-0.172-0.0242-0.17266.3217-15.3349-19.9111
31.21450.07110.1291.21930.03840.68-0.00530.2962-0.174-0.14450.00350.07190.18820.14170.00170.00060.0327-0.0322-0.0799-0.104-0.14485.3385-15.708-61.8254
40.65370.0075-0.00471.1708-0.19940.9995-0.044-0.01910.22380.20670.0062-0.2507-0.15510.27760.0379-0.0749-0.0484-0.0902-0.1058-0.053-0.053123.807118.495-36.9897
50.6005-0.1411-0.04071.21970.14091.02380.0137-0.08570.2912-0.14290.063-0.3591-0.15310.0546-0.0767-0.0421-0.07420.0207-0.2073-0.09780.06749.988720.400246.8259
60.5407-0.03170.04820.86370.12950.83110.0450.0722-0.0371-0.45810.0014-0.13750.2111-0.0509-0.04640.2656-0.06260.0545-0.2289-0.0249-0.1834-0.2068-16.604420.5452
71.2418-0.08020.1371.0652-0.18190.5861-0.0082-0.2916-0.09540.06530.0313-0.14450.1525-0.0546-0.02310.0086-0.0642-0.0438-0.08010.0072-0.13720.5591-16.806662.366
80.7144-0.1965-0.03731.09710.12330.7930.0163-0.00470.0966-0.2189-0.01750.2846-0.0295-0.31040.0012-0.037-0.0681-0.081-0.0703-0.0116-0.092-29.15988.230837.4424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|366 - A|813 }
2X-RAY DIFFRACTION2{ A|831 - A|1227 }
3X-RAY DIFFRACTION3{ B|365 - B|816 }
4X-RAY DIFFRACTION4{ B|831 - B|1227 }
5X-RAY DIFFRACTION5{ C|365 - C|814 }
6X-RAY DIFFRACTION6{ C|830 - C|1227 }
7X-RAY DIFFRACTION7{ D|367 - D|816 }
8X-RAY DIFFRACTION8{ D|831 - D|1227 }

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