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

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Basic information

Entry
Database: PDB / ID: 3zhu
TitleCrystal structure of the SucA domain of Mycobacterium smegmatis KGD, second post-decarboxylation intermediate from 2-oxoadipate
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-TD8 / 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)391,09016
Polymers388,6674
Non-polymers2,42312
Water16,826934
1
C: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
D: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5458
Polymers194,3332
Non-polymers1,2126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-52.8 kcal/mol
Surface area57320 Å2
MethodPISA
2
A: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
B: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5458
Polymers194,3332
Non-polymers1,2126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-54.5 kcal/mol
Surface area57160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.783, 82.286, 163.039
Angle α, β, γ (deg.)99.19, 99.10, 100.71
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.257, 0.1378, 0.9565), (0.135, -0.9749, 0.1768), (0.9569, 0.1746, 0.2319)-0.1642, -0.1244, 0.2798
2given(0.1962, 0.2198, -0.9556), (0.2292, -0.9578, -0.1733), (-0.9534, -0.185, -0.2384)-77.5477, 12.4499, 3.4088
3given(-0.9312, -0.3646, -0.0054), (-0.3646, 0.9312, -0.0045), (0.0067, -0.0022, -1)24.6803, -22.3424, -71.096

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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-OXOGL 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
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-TD8 / (5R)-5-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-5-(2-{[(phosphonatooxy)phosphinato]oxy}ethyl)-1,3-thiazol-3-ium-2-yl}-5-hydroxypentanoate


Mass: 541.430 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N4O10P2S
#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.: 934 / 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: 2.63 Å3/Da / Density % sol: 53.2 % / 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→41.85 Å / Num. obs: 169497 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 39.96 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 92

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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 2YID

2yid


Resolution: 2.3→40.36 Å / Cor.coef. Fo:Fc: 0.9192 / Cor.coef. Fo:Fc free: 0.8925 / SU R Cruickshank DPI: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.293 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.218
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=27172. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=27172. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 8505 5.02 %RANDOM
Rwork0.1999 ---
obs0.2017 169477 96.68 %-
Displacement parametersBiso mean: 41.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.9527 Å2-0.024 Å21.8267 Å2
2--1.9189 Å20.0475 Å2
3----2.8717 Å2
Refine analyzeLuzzati coordinate error obs: 0.287 Å
Refinement stepCycle: LAST / Resolution: 2.3→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26090 0 144 934 27168
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0126767HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0436309HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12378SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes695HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3955HARMONIC5
X-RAY DIFFRACTIONt_it26767HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion2.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3457SEMIHARMONIC5
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_contact32813SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 597 5.02 %
Rwork0.1995 11303 -
all0.2013 11900 -
obs--96.68 %
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)
10.6921-0.01290.22791.2330.12160.23990.08270.1447-0.049-0.2777-0.07580.01090.16610.0908-0.00690.15780.1479-0.0491-0.1252-0.0569-0.22941.6854-17.6457-18.4277
20.52970.00220.06820.9077-0.16020.53770.02490.02950.18790.0672-0.0446-0.2851-0.02190.17620.0197-0.07740.069-0.0229-0.1014-0.0225-0.043419.775817.4914.5271
30.3507-0.30880.15371.2825-0.09560.79690.02090.0210.0335-0.0849-0.01790.21750.0137-0.0672-0.0030.02630.0944-0.0717-0.1433-0.0202-0.1215-20.709614.2174-5.1325
40.37650.01040.14040.8412-0.07090.60850.0194-0.0337-0.01780.1037-0.0191-0.02450.10180.0715-0.00030.16880.1285-0.0513-0.1283-0.0266-0.20821.2006-13.192523.2376
50.2602-0.17040.13131.27930.16240.7734-0.037-0.0270.11580.06090.019-0.1384-0.01930.0880.0180.02730.0458-0.0747-0.1435-0.0358-0.116629.090250.4695-65.4471
60.3965-0.1369-0.00520.79540.18070.74260.01980.0843-0.0179-0.1451-0.04920.05010.10340.00180.02940.16310.0637-0.0556-0.159-0.013-0.202119.132216.611-94.2367
70.5662-0.20670.13571.0009-0.05850.0949-0.0348-0.1048-0.04050.29680.0020.03960.1256-0.04070.03280.13590.0702-0.0189-0.12630.0037-0.195820.098112.6379-52.5991
80.6094-0.2523-0.0781.15580.18930.5644-0.01630.01520.0021-0.085-0.05890.4222-0.0392-0.16110.0752-0.10650.0392-0.0346-0.1329-0.0469-0.0045-9.436638.1244-75.7422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|361 - A|810 }
2X-RAY DIFFRACTION2{ A|815 - A|1227 }
3X-RAY DIFFRACTION3{ B|365 - B|810 }
4X-RAY DIFFRACTION4{ B|811 - B|1227 }
5X-RAY DIFFRACTION5{ C|364 - C|810 }
6X-RAY DIFFRACTION6{ C|811 - C|1227 }
7X-RAY DIFFRACTION7{ D|361 - D|810 }
8X-RAY DIFFRACTION8{ D|811 - D|1227 }

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