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- PDB-2y0p: Crystal structure of the SucA domain of Mycobacterium smegmatis a... -

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Basic information

Entry
Database: PDB / ID: 2y0p
TitleCrystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase in complex with the enamine-ThDP intermediate and acetyl-CoA
Components2-OXOGLUTARATE DECARBOXYLASE
KeywordsLYASE / KDH / KGD / 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
ACETYL COENZYME *A / Chem-TD7 / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionDec 7, 2010Deposition 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)394,10816
Polymers388,6674
Non-polymers5,44112
Water9,260514
1
A: 2-OXOGLUTARATE DECARBOXYLASE
B: 2-OXOGLUTARATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,0548
Polymers194,3332
Non-polymers2,7216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-46 kcal/mol
Surface area56340 Å2
MethodPISA
2
C: 2-OXOGLUTARATE DECARBOXYLASE
D: 2-OXOGLUTARATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,0548
Polymers194,3332
Non-polymers2,7216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13050 Å2
ΔGint-36.1 kcal/mol
Surface area56430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.062, 81.953, 161.876
Angle α, β, γ (deg.)99.26, 97.09, 100.58
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1753, 0.1515, 0.9728), (0.148, -0.9728, 0.1782), (0.9733, 0.1752, 0.1481)-0.2236, -0.0334, 0.2442
2given(0.1012, 0.2015, -0.9742), (0.2067, -0.9622, -0.1775), (-0.9731, -0.1834, -0.139)-76.47, 12.5711, 8.1076
3given(-0.9343, -0.3563, 0.0135), (-0.3563, 0.9344, -0.0001), (-0.0126, -0.0049, -0.9999)23.1382, -22.4737, -70.7349

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Components

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


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: MC2 155 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)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-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.73 Å3/Da / Density % sol: 54.9 % / 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: 2.4→41.4 Å / Num. obs: 149496 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 41.18 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.9 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XT7

2xt7
PDB Unreleased entry


Resolution: 2.4→35.14 Å / Cor.coef. Fo:Fc: 0.9291 / Cor.coef. Fo:Fc free: 0.9132 / SU R Cruickshank DPI: 0.381 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.346 / SU Rfree Blow DPI: 0.217 / SU Rfree Cruickshank DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 7517 5.03 %RANDOM
Rwork0.1968 ---
obs0.198 149475 95.79 %-
Displacement parametersBiso mean: 44.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.6692 Å2-1.5954 Å25.2656 Å2
2---0.0948 Å2-0.0061 Å2
3---2.764 Å2
Refine analyzeLuzzati coordinate error obs: 0.329 Å
Refinement stepCycle: LAST / Resolution: 2.4→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25968 0 327 514 26809
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00826835HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9736474HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12205SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes712HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3972HARMONIC5
X-RAY DIFFRACTIONt_it26699HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion2.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3481SEMIHARMONIC5
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_contact32116SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2428 510 4.63 %
Rwork0.2209 10510 -
all0.222 11020 -
obs--95.79 %
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)
10.47640.12910.23371.01050.32730.90480.03960.09730.0181-0.01260.1079-0.17720.20960.2571-0.1475-0.04850.0915-0.0437-0.1592-0.0493-0.12049.9105-0.7972-8.1227
20.483-0.17360.35180.7434-0.08140.87990.0076-0.05290.04640.11280.0281-0.00990.1953-0.0093-0.03560.06550.0644-0.0769-0.1853-0.0299-0.1308-9.7340.82689.1523
30.37690.03210.27760.62460.11030.8799-0.00810.01550.0622-0.13770.01940.02240.0770.0405-0.01130.13370.0433-0.1092-0.20290.022-0.134821.913733.3873-79.1672
40.4638-0.29850.28810.9755-0.34350.8910.0379-0.067-0.0322-0.04120.09470.21550.1903-0.2099-0.1325-0.0114-0.0025-0.0675-0.15380.0769-0.13383.538724.8193-62.9967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN B)
3X-RAY DIFFRACTION3(CHAIN C)
4X-RAY DIFFRACTION4(CHAIN D)

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