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- PDB-6r2a: Crystal structure of the SucA domain of Mycobacterium smegmatis K... -

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Basic information

Entry
Database: PDB / ID: 6r2a
TitleCrystal structure of the SucA domain of Mycobacterium smegmatis KGD cocrystallized 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-ZP1 / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,41214
Polymers194,3332
Non-polymers2,07912
Water22,8611269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12650 Å2
ΔGint-104 kcal/mol
Surface area59610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.480, 108.020, 120.530
Angle α, β, γ (deg.)90.00, 103.55, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2
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-ZP1 / (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-[ethoxy(oxidanyl)phosphoryl]-4-oxidanyl-butanoic acid


Mass: 636.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H31N4O13P3S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1269 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 2% 2-methyl-2-propanol, 47% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.7→40.37 Å / Num. obs: 232526 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.91 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.042 / Net I/σ(I): 11.8
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 32854 / CC1/2: 0.792 / Rpim(I) all: 0.327 / % possible all: 95.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YID

2yid


Resolution: 1.7→40.37 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.077 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.072
RfactorNum. reflection% reflectionSelection details
Rfree0.168 11650 5.01 %RANDOM
Rwork0.151 ---
obs0.152 232481 98.5 %-
Displacement parametersBiso mean: 31.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.8872 Å20 Å20.8393 Å2
2---1.1585 Å20 Å2
3---2.0456 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→40.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13296 0 130 1269 14695
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113851HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9318826HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6523SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2449HARMONIC5
X-RAY DIFFRACTIONt_it13851HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion2.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1781SEMIHARMONIC5
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_contact17483SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.71 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2902 217 4.67 %
Rwork0.2333 4433 -
all0.2359 4650 -
obs--89.78 %
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)
10.5121-0.03550.06790.4701-0.00370.4388-0.01390.0954-0.0256-0.00430.0208-0.08360.04440.1173-0.0069-0.04720.00840.00080.0035-0.0071-0.022848.944112.5159.7987
20.75250.02590.22850.516-0.01170.7475-0.04850.03470.18320.0210.02330.1957-0.109-0.2270.0252-0.12240.04370.0082-0.0430.0281-0.00358.462131.673916.6583
30.37160.00870.09910.63540.0270.6290.0068-0.0727-0.1150.13630.03010.09970.1771-0.1049-0.0369-0.0019-0.02560.0286-0.06970.0395-0.055721.609-3.445936.6857
40.6458-0.01060.1750.4820.02150.9805-0.0419-0.13930.21680.19360.0084-0.0243-0.2210.04640.03350.0107-0.0029-0.0153-0.0995-0.0536-0.054139.482938.794641.4947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|366 - A|810 }
2X-RAY DIFFRACTION2{ A|811 - A|1227 }
3X-RAY DIFFRACTION3{ B|360 - B|810 }
4X-RAY DIFFRACTION4{ B|811 - B|1227 }

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