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- PDB-6r2b: Crystal structure of the SucA domain of Mycobacterium smegmatis K... -

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Basic information

Entry
Database: PDB / ID: 6r2b
TitleCrystal structure of the SucA domain of Mycobacterium smegmatis KGD after soaking with succinylphosphonate
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-QSP / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.96 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

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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)391,35816
Polymers388,6674
Non-polymers2,69112
Water24,5001360
1
A: Multifunctional 2-oxoglutarate metabolism enzyme
B: Multifunctional 2-oxoglutarate metabolism enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6798
Polymers194,3332
Non-polymers1,3466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-52 kcal/mol
Surface area57800 Å2
MethodPISA
2
C: Multifunctional 2-oxoglutarate metabolism enzyme
D: Multifunctional 2-oxoglutarate metabolism enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6798
Polymers194,3332
Non-polymers1,3466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-54 kcal/mol
Surface area57560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.120, 82.760, 162.970
Angle α, β, γ (deg.)98.55, 97.52, 102.18
Int Tables number1
Space group name H-MP1

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Components

#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
#2: Chemical
ChemComp-QSP / (4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-oxidanyl-4-phosphono-butanoic acid


Mass: 608.391 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H27N4O13P3S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1360 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
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: 1.96→158.88 Å / Num. obs: 284499 / % possible obs: 97.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 28.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.052 / Net I/σ(I): 8.6
Reflection shellResolution: 1.96→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 14077 / CC1/2: 0.8 / Rpim(I) all: 0.344 / % possible all: 96.6

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Processing

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

2yid


Resolution: 1.96→158.87 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.175 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.245 14368 5.05 %RANDOM
Rwork0.228 ---
obs0.229 284471 97.1 %-
Displacement parametersBiso mean: 33.33 Å2
Baniso -1Baniso -2Baniso -3
1--4.8456 Å2-0.54 Å21.0042 Å2
2--0.3602 Å20.6368 Å2
3---4.4854 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.96→158.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26203 0 156 1360 27719
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0126915HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9836506HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12528SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4708HARMONIC5
X-RAY DIFFRACTIONt_it26915HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion2.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3455SEMIHARMONIC5
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_contact32750SEMIHARMONIC4
LS refinement shellResolution: 1.96→1.98 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2531 276 4.85 %
Rwork0.2131 5414 -
all0.215 5690 -
obs--93.63 %
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)
10.3626-0.00490.07480.66680.15460.3904-0.00190.0497-0.0516-0.1597-0.00970.04110.13080.0530.01170.10030.0677-0.0419-0.118-0.0328-0.10461.9884-17.0857-17.9879
20.4570.0312-0.0330.6273-0.15320.5449-0.0017-0.04360.13140.0351-0.0256-0.1378-0.11440.13660.0274-0.00050.0261-0.0428-0.0887-0.0395-0.031418.037319.18453.4342
30.3147-0.22270.13460.5028-0.03430.68170.00790.00370.0689-0.0733-0.00030.1126-0.0813-0.0945-0.00760.02180.0842-0.0589-0.1123-0.0079-0.0281-22.189414.1125-5.0827
40.31870.01430.05970.4317-0.09430.7051-0.0008-0.0675-0.00970.1060.01510.02730.06630.0487-0.01430.0640.0846-0.0312-0.0878-0.0217-0.09381.041-12.654422.9294
50.1820.00350.16820.68780.07280.76-0.0261-0.01420.10920.04670.0318-0.0737-0.1210.0545-0.0057-0.00030.0451-0.0355-0.1143-0.0449-0.015527.519849.4821-65.7263
60.3794-0.07390.0410.37920.15980.77250.03860.0751-0.0167-0.1004-0.017-0.0210.0848-0.0192-0.02160.05060.0611-0.0257-0.0932-0.0198-0.079817.341215.5885-94.2318
70.4046-0.09160.16810.5915-0.00980.4566-0.0088-0.047-0.04650.10580.0148-0.04070.1785-0.0072-0.0060.07040.0712-0.041-0.103-0.0026-0.092618.081610.9419-53.6501
80.5814-0.1447-0.09840.59830.22060.74070.01110.03370.0362-0.0136-0.06320.1538-0.0422-0.22440.0521-0.06030.0702-0.0264-0.0288-0.0232-0.0425-11.22737.6346-74.8386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|362 - A|827}
2X-RAY DIFFRACTION2{A|830 - A|1227}
3X-RAY DIFFRACTION3{B|365 - B|810}
4X-RAY DIFFRACTION4{B|811 - B|1227}
5X-RAY DIFFRACTION5{C|365 - C|810}
6X-RAY DIFFRACTION6{C|811 - C|1227}
7X-RAY DIFFRACTION7{D|367 - D|827}
8X-RAY DIFFRACTION8{D|830 - D|1227}

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