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- PDB-6i2r: Crystal structure of the SucA domain of Mycobacterium smegmatis K... -

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Basic information

Entry
Database: PDB / ID: 6i2r
TitleCrystal structure of the SucA domain of Mycobacterium smegmatis KGD (alpha-ketoglutarate decarboxylase), mutant R802A, in complex with GarA
Components
  • Glycogen accumulation regulator GarA
  • Multifunctional 2-oxoglutarate metabolism enzyme
KeywordsOXIDOREDUCTASE / oxoglutarate dehydrogenase / 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 / mRNA binding / 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 / Tumour Suppressor Smad4 - #20 ...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 / Tumour Suppressor Smad4 - #20 / 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 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Chloramphenicol acetyltransferase-like domain superfamily / Thiamin diphosphate-binding fold / SMAD/FHA domain superfamily / Helix Hairpins / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Glycogen accumulation regulator GarA / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWagner, T. / Bellinzoni, M. / Alzari, P.M.
CitationJournal: Sci.Signal. / Year: 2019
Title: Structural insights into the functional versatility of an FHA domain protein in mycobacterial signaling.
Authors: Wagner, T. / Andre-Leroux, G. / Hindie, V. / Barilone, N. / Lisa, M.N. / Hoos, S. / Raynal, B. / Vulliez-Le Normand, B. / O'Hare, H.M. / Bellinzoni, M. / Alzari, P.M.
History
DepositionNov 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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 / 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 / _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: Glycogen accumulation regulator GarA
C: Multifunctional 2-oxoglutarate metabolism enzyme
D: Glycogen accumulation regulator GarA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,36510
Polymers218,3864
Non-polymers9796
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15370 Å2
ΔGint-88 kcal/mol
Surface area62840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.745, 143.145, 167.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#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: 97080.531 Da / Num. of mol.: 2 / Mutation: R802A
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: Protein Glycogen accumulation regulator GarA


Mass: 12112.292 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: garA, MSMEG_3647, MSMEI_3561 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QYG2

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Non-polymers , 4 types, 460 molecules

#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM Hepes-Na pH 7.5, 47% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.2→48.15 Å / Num. obs: 113280 / % possible obs: 96.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 32.31 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.039 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.746 / Rpim(I) all: 0.526

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Processing

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

2yic


Resolution: 2.2→48.15 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.222 / SU Rfree Blow DPI: 0.173 / SU Rfree Cruickshank DPI: 0.175
RfactorNum. reflection% reflectionSelection details
Rfree0.219 5699 5.05 %RANDOM
Rwork0.195 ---
obs0.196 112917 96.6 %-
Displacement parametersBiso mean: 35.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.9858 Å20 Å20 Å2
2---2.394 Å20 Å2
3---0.4083 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.2→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14168 0 56 454 14678
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114514HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0119681HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6712SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2544HARMONIC5
X-RAY DIFFRACTIONt_it14514HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion2.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1875SEMIHARMONIC5
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_contact17440SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2917 343 5.47 %
Rwork0.2762 5932 -
all0.2771 6275 -
obs--73.46 %
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)
10.73110.05070.09250.5827-0.18540.44490.0063-0.1088-0.10710.12880.0252-0.01480.0878-0.0214-0.03150.04970.0199-0.0221-0.07970.0092-0.09319.4102-16.956115.5144
20.59940.043-0.04060.5904-0.00580.5278-0.01780.07730.0662-0.08130.0235-0.0691-0.03920.0393-0.00570.0136-0.02090.0074-0.0454-0.0062-0.07412.728513.5918-19.4778
32.1330.0033-0.16511.868-0.64013.40720.1062-0.0369-0.1768-0.034-0.0529-0.21450.00460.4084-0.0533-0.03010.0184-0.05070.0272-0.0392-0.118837.3864-13.566232.3587
40.7464-0.00820.03020.79280.06770.3393-0.02730.1046-0.1459-0.13980.07090.06880.1008-0.0421-0.04360.0304-0.0693-0.036-0.093-0.0181-0.089-12.8906-20.1955-18.2813
50.4965-0.16120.05750.7704-0.02320.3851-0.0479-0.09070.05140.13460.06010.1565-0.0621-0.1155-0.0123-0.00980.03080.0341-0.0464-0.0045-0.0762-15.827516.351510.7659
64.7731-0.13091.73572.27450.34782.976-0.03180.2405-0.2316-0.29710.05360.4885-0.1479-0.4076-0.0218-0.0809-0.0968-0.17930.04240.0458-0.0809-40.5972-19.7922-36.3132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|364 - A|813 }
2X-RAY DIFFRACTION2{ A|829 - A|1227 }
3X-RAY DIFFRACTION3{ B|54 - B|147 }
4X-RAY DIFFRACTION4{ C|361 - C|813 }
5X-RAY DIFFRACTION5{ C|832 - C|1227 }
6X-RAY DIFFRACTION6{ D|56 - D|147 }

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