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- PDB-2yid: Crystal structure of the SucA domain of Mycobacterium smegmatis a... -

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Basic information

Entry
Database: PDB / ID: 2yid
TitleCrystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase in complex with the enamine-ThDP intermediate
Components2-OXOGLUTARATE DECARBOXYLASE
KeywordsLYASE / THDP-COVALENT ADDUCT
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 / thiamine pyrophosphate binding / tricarboxylic acid cycle / magnesium ion binding
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-TD7 / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWagner, T. / Bellinzoni, M. / Wehenkel, A.M. / O'Hare, H.M. / Alzari, P.M.
CitationJournal: Chem.Biol. / Year: 2011
Title: Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism.
Authors: Wagner, T. / Bellinzoni, M. / Wehenkel, A.M. / O'Hare, H.M. / Alzari, P.M.
History
DepositionMay 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references / Version format compliance
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: 2-OXOGLUTARATE DECARBOXYLASE
B: 2-OXOGLUTARATE DECARBOXYLASE
C: 2-OXOGLUTARATE DECARBOXYLASE
D: 2-OXOGLUTARATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,03016
Polymers388,6674
Non-polymers2,36312
Water13,151730
1
A: 2-OXOGLUTARATE DECARBOXYLASE
B: 2-OXOGLUTARATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5158
Polymers194,3332
Non-polymers1,1826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-52.1 kcal/mol
Surface area57230 Å2
MethodPISA
2
C: 2-OXOGLUTARATE DECARBOXYLASE
D: 2-OXOGLUTARATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5158
Polymers194,3332
Non-polymers1,1826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11330 Å2
ΔGint-54.1 kcal/mol
Surface area57860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.843, 82.287, 163.478
Angle α, β, γ (deg.)99.23, 99.03, 100.63
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2577, 0.1372, 0.9564), (0.1343, -0.9752, 0.1761), (0.9569, 0.1738, 0.2328)-0.245, -0.2656, 0.2854
2given(0.1998, 0.2184, -0.9552), (0.2255, -0.9589, -0.1721), (-0.9535, -0.1811, -0.2409)-77.8178, 12.5675, 3.0225
3given(-0.9328, -0.3602, -0.0052), (-0.3602, 0.9329, -0.005), (0.0066, -0.0028, -1)24.5672, -22.6967, -71.2941

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Components

#1: Protein
2-OXOGLUTARATE DECARBOXYLASE / / 2-OXOGLUTARATE CARBOXY-LYASE / ALPHA-KETOGLUTARATE DECARBOXYLASE / KDH


Mass: 97166.648 Da / Num. of mol.: 4 / Fragment: RESIDUES 361-1227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: A0R2B1, 2-oxoglutarate decarboxylase
#2: Chemical
ChemComp-TD7 / (4E)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-2(3H)-ylidene}-4-hydroxybutanoic acid


Mass: 526.395 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H24N4O10P2S
#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 / Water


Mass: 18.015 Da / Num. of mol.: 730 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST GLY 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: 2.71 Å3/Da / Density % sol: 54.6 % / Description: NONE
Crystal growpH: 7.6
Details: 52% MPD, 20 MM SODIUM ACETATE, 5% 1,3-PROPANEDIOL., pH 7.6

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 20, 2010 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.25→41.9 Å / Num. obs: 179918 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 30.43 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.9
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 94.6

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YIC

2yic


Resolution: 2.25→32.94 Å / Cor.coef. Fo:Fc: 0.9262 / Cor.coef. Fo:Fc free: 0.9014 / SU R Cruickshank DPI: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.251 / SU Rfree Blow DPI: 0.19 / SU Rfree Cruickshank DPI: 0.197
Details: NCS REPRESENTATION : RESTRAINT LSSR (-AUTONCS) IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=26979. ...Details: NCS REPRESENTATION : RESTRAINT LSSR (-AUTONCS) IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=26979. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 9062 5.04 %RANDOM
Rwork0.192 ---
obs0.1935 179896 95.71 %-
Displacement parametersBiso mean: 33.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.8828 Å21.1116 Å2-0.4018 Å2
2--4.5879 Å20.5883 Å2
3----3.7051 Å2
Refine analyzeLuzzati coordinate error obs: 0.295 Å
Refinement stepCycle: LAST / Resolution: 2.25→32.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26102 0 140 730 26972
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0126777HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0136320HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12397SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes700HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3959HARMONIC5
X-RAY DIFFRACTIONt_it26777HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion2.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3454SEMIHARMONIC5
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_contact32619SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2488 668 5.08 %
Rwork0.2129 12469 -
all0.2147 13137 -
obs--95.71 %
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)
10.46260.03590.02640.86960.0890.35030.02740.04640.0125-0.0565-0.0386-0.04170.09170.0920.0112-0.06330.0802-0.0112-0.0981-0.0238-0.14310.4136-0.6089-7.2293
20.3503-0.21980.13250.6865-0.21410.4986-0.0015-0.00270.02030.0628-0.01210.1350.03270.00790.0136-0.02920.0467-0.0054-0.126-0.0589-0.0854-9.86270.5688.9737
30.5163-0.27290.10980.9142-0.0230.3668-0.0445-0.0424-0.00580.12390.00540.1480.0493-0.04780.0391-0.080.01840.0159-0.1165-0.0189-0.11265.63725.4353-64.096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN D

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