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- PDB-6g74: Structure of the Y21F variant of quinolinate synthase in complex ... -

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Basic information

Entry
Database: PDB / ID: 6g74
TitleStructure of the Y21F variant of quinolinate synthase in complex with phthalate
ComponentsQuinolinate synthase A
KeywordsTRANSFERASE / NAD BIOSYNTHESIS / IRON SULFUR CLUSTER
Function / homology
Function and homology information


quinolinate synthase / quinolinate synthetase A activity / 'de novo' NAD+ biosynthetic process from L-aspartate / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
NadA-like / Quinolinate synthetase A / Quinolinate synthase A, type 2 / Quinolinate synthetase A superfamily / Quinolinate synthetase A protein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHTHALIC ACID / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
Funding support France, 1items
OrganizationGrant numberCountry
ANR-16-CE18-0026 France
Citation
Journal: ACS Chem. Biol. / Year: 2018
Title: Crystallographic Trapping of Reaction Intermediates in Quinolinic Acid Synthesis by NadA.
Authors: Volbeda, A. / Saez Cabodevilla, J. / Darnault, C. / Gigarel, O. / Han, T.H. / Renoux, O. / Hamelin, O. / Ollagnier-de-Choudens, S. / Amara, P. / Fontecilla-Camps, J.C.
#1: Journal: J. Am. Chem. Soc. / Year: 2016
Title: Crystal Structures of Quinolinate Synthase in Complex with a Substrate Analogue, the Condensation Intermediate, and Substrate-Derived Product.
Authors: Volbeda, A. / Darnault, C. / Renoux, O. / Reichmann, D. / Amara, P. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C.
#2: Journal: J. Am. Chem. Soc. / Year: 2014
Title: The crystal structure of Fe4S4 quinolinate synthase unravels an enzymatic dehydration mechanism that uses tyrosine and a hydrolase-type triad.
Authors: Cherrier, M.V. / Chan, A. / Darnault, C. / Reichmann, D. / Amara, P. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C.
History
DepositionApr 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 17, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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: Quinolinate synthase A
B: Quinolinate synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0546
Polymers69,0192
Non-polymers1,0364
Water7,440413
1
A: Quinolinate synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0273
Polymers34,5091
Non-polymers5182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Quinolinate synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0273
Polymers34,5091
Non-polymers5182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.140, 52.160, 58.950
Angle α, β, γ (deg.)103.820, 90.630, 90.370
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Quinolinate synthase A


Mass: 34509.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: nadA, TM_1644 / Plasmid: PT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1X7, quinolinate synthase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-PHT / PHTHALIC ACID


Mass: 166.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG3350, TRIS, KCL, HEPES, PHTHALATE, Na2HPO4, ANAEROBIC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2→49.13 Å / Num. obs: 34665 / % possible obs: 90.2 % / Redundancy: 2.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.044 / Rrim(I) all: 0.072 / Net I/σ(I): 12.1 / Num. measured all: 82582
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.072.40.27634650.8980.2170.35391.9
7.75-49.132.60.0315740.9970.0230.03987.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P3X (OPEN FORM) AND 5LQM (CLOSED FORM)

4p3x

5lqm


Resolution: 2→43.43 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.989 / SU ML: 0.172 / SU R Cruickshank DPI: 0.3231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.21
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1831 5.3 %RANDOM
Rwork0.1896 ---
obs0.1919 32832 90.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.59 Å2 / Biso mean: 31.326 Å2 / Biso min: 14.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.02 Å2-0.47 Å2
2--1.25 Å2-1.95 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 2→43.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 40 414 5265
Biso mean--31.16 39.43 -
Num. residues----608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195664
X-RAY DIFFRACTIONr_bond_other_d0.0010.025487
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9927686
X-RAY DIFFRACTIONr_angle_other_deg1.923312821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2535717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15624.854239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.301151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3751526
X-RAY DIFFRACTIONr_chiral_restr0.0910.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216165
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021029
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 125 -
Rwork0.272 2540 -
all-2665 -
obs--92.86 %
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)
10.7465-0.4189-0.34740.50980.02841.08760.0409-0.0266-0.03580.00260.03020.0770.13610.051-0.07110.0483-0.0006-0.01650.01470.00970.0246-20.7351-11.59296.5454
20.7198-0.0156-0.75130.5193-0.33261.53670.1122-0.01870.0286-0.0055-0.0472-0.0111-0.05560.0101-0.0650.0307-0.00310.0050.0110.00710.0092-33.16159.8672-0.4764
30.57870.4039-0.02370.73240.17410.59580.02690.0066-0.0511-0.02150.0053-0.0431-0.048-0.0569-0.03220.00680.0052-0.00070.0217-0.00420.0098-26.8656-7.7415-18.4627
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 80
2X-RAY DIFFRACTION1A254 - 279
3X-RAY DIFFRACTION2A81 - 167
4X-RAY DIFFRACTION2A280 - 298
5X-RAY DIFFRACTION3A168 - 253

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