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- PDB-3zhv: Crystal structure of the SucA domain of Mycobacterium smegmatis K... -

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Basic information

Entry
Database: PDB / ID: 3zhv
TitleCrystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)
ComponentsMULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
KeywordsOXIDOREDUCTASE / E1O
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-TDW / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWagner, T. / Barilone, N. / Bellinzoni, M. / Alzari, P.M.
CitationJournal: Biochem.J. / Year: 2014
Title: A Dual Conformation of the Post-Decarboxylation Intermediate is Associated with Distinct Enzyme States in Mycobacterial Alpha-Ketoglutarate Decarboxylase (Kgd).
Authors: Wagner, T. / Barilone, N. / Alzari, P.M. / Bellinzoni, M.
History
DepositionDec 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)390,80216
Polymers388,6674
Non-polymers2,13512
Water17,457969
1
C: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
D: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,4018
Polymers194,3332
Non-polymers1,0686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-90.2 kcal/mol
Surface area54970 Å2
MethodPISA
2
A: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
B: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,4018
Polymers194,3332
Non-polymers1,0686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-87.5 kcal/mol
Surface area54890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.464, 83.702, 160.333
Angle α, β, γ (deg.)99.68, 98.87, 100.63
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2039, 0.0664, 0.9767), (0.0656, -0.9945, 0.0813), (0.9768, 0.0806, 0.1985)45.7898, 4.5086, -37.6023
2given(-0.9324, -0.3615, -0.005), (-0.3615, 0.9324), (0.0047, 0.0018, -1)0.0626, 0.0803, 0.6692
3given(0.1686, 0.1401, -0.9757), (0.302, -0.9496, -0.0841), (-0.9383, -0.2804, -0.2024)46.4174, 4.6166, -37.4354

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Components

#1: Protein
MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME / 2-HYDROXY-3-OXOADIPATE SYNTHASE / HOA SYNTHASE / HOAS / 2-OXOGLUTARATE CARBOXY-LYASE / 2- ...2-HYDROXY-3-OXOADIPATE SYNTHASE / HOA SYNTHASE / HOAS / 2-OXOGLUTARATE CARBOXY-LYASE / 2-OXOGLUTARATE DECARBOXYLASE / ALPHA-KETOGLUTARATE DECARBOXYLASE / KG DECARBOXYLASE / KGD / ALPHA-KETOGLUTARATE-GLYOXYLATE CARBOLIGASE / 2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT / ODH E1 COMPONENT / ALPHA-KETOGLUTARATE DEHYDROGENASE E1 COMPONENT / KDH E1 COMPONENT / DIHYDROLIPOYLLYSINE-RESIDUE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX / 2-OXOGLUTARATE DEHYDROGENASE COMPLEX E2 COMPONENT / ODH E2 COMPONENT / OGDC-E2 / DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE


Mass: 97166.648 Da / Num. of mol.: 4 / Fragment: SUCA-LIKE CATALYTIC DOMAIN, RESIDUES 361-1227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2_155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: A0R2B1, 2-hydroxy-3-oxoadipate synthase, 2-oxoglutarate decarboxylase, oxoglutarate dehydrogenase (succinyl-transferring), dihydrolipoyllysine-residue succinyltransferase
#2: Chemical
ChemComp-TDW / 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-[(1S)-1-oxidanylethyl]-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen phosphate


Mass: 469.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H23N4O8P2S
#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.: 969 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TER FIRST GLYCINE RESIDUE IS A PURIFICATION TAG LEFTOVER (TEV CLEAVAGE SITE)

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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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: NONE
Crystal growpH: 7 / Details: 59% MPD, 22.5 MM NA ACETATE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.3→41.86 Å / Num. obs: 172580 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 46.53 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YIC

2yic


Resolution: 2.3→41.06 Å / Cor.coef. Fo:Fc: 0.9326 / Cor.coef. Fo:Fc free: 0.9144 / SU R Cruickshank DPI: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.277 / SU Rfree Blow DPI: 0.205 / SU Rfree Cruickshank DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 8626 5 %RANDOM
Rwork0.2034 ---
obs0.205 172547 97.63 %-
Displacement parametersBiso mean: 50.37 Å2
Baniso -1Baniso -2Baniso -3
1--7.4557 Å20.8742 Å2-2.2454 Å2
2--2.7212 Å20.174 Å2
3---4.7344 Å2
Refine analyzeLuzzati coordinate error obs: 0.331 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25040 0 124 969 26133
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125678HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0134858HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11797SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes642HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3870HARMONIC5
X-RAY DIFFRACTIONt_it25678HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion2.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3340SEMIHARMONIC5
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_contact31052SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2508 617 4.86 %
Rwork0.2085 12069 -
all0.2105 12686 -
obs--97.63 %
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)
10.6893-0.25360.15431.3385-0.37751.0636-0.02110.0750.13720.04910.09430.3932-0.0315-0.098-0.0732-0.12710.17430.0194-0.12960.07720.0103-16.831915.0313-46.6424
20.5347-0.11530.11160.7331-0.12390.7081-0.0212-0.1109-0.05870.25660.0550.06850.17830.1073-0.03380.16750.26820.0501-0.1070.0331-0.18716.2948-15.3502-19.9064
31.07450.0150.10271.17760.03150.7697-0.00080.2863-0.1623-0.20990.04340.11320.2280.127-0.04260.00190.187-0.0198-0.0317-0.0416-0.20215.0431-15.2856-62.0029
40.7710.1979-0.01741.2398-0.31930.5741-0.0404-0.020.2130.18080.0268-0.2349-0.08280.22190.0136-0.08920.1827-0.0324-0.0329-0.0122-0.084823.956418.6238-36.7647
50.6608-0.06910.08710.94390.05540.8506-0.0581-0.12340.2767-0.04740.0362-0.2625-0.1290.07720.02180.01280.0822-0.021-0.2057-0.0502-0.00979.691720.479646.9948
60.6652-0.10720.03480.67650.15370.69270.01030.0947-0.0397-0.3166-0.0029-0.09110.1498-0.0145-0.00740.2570.09380.0595-0.2030.0062-0.1946-0.2882-16.743320.5176
71.178-0.19470.10961.1032-0.21610.6107-0.0499-0.2699-0.11340.07940.0283-0.12870.1396-0.04680.02150.03590.1162-0.0145-0.0880.0526-0.18260.4999-16.489662.4914
80.8944-0.3295-0.09861.10840.07490.7407-0.0138-0.00410.072-0.1330.00020.2125-0.0412-0.23220.0136-0.01480.0823-0.0546-0.09490.0098-0.1225-29.11968.407337.248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 365-810
2X-RAY DIFFRACTION2CHAIN A AND RESID 831-1227
3X-RAY DIFFRACTION3CHAIN B AND RESID 365-810
4X-RAY DIFFRACTION4CHAIN B AND RESID 831-1227
5X-RAY DIFFRACTION5CHAIN C AND RESID 367-810
6X-RAY DIFFRACTION6CHAIN C AND RESID 831-1227
7X-RAY DIFFRACTION7CHAIN D AND RESID 366-810
8X-RAY DIFFRACTION8CHAIN D AND RESID 831-1227

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