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- PDB-4zdk: Crystal structure of the M. tuberculosis CTP synthase PyrG in com... -

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Basic information

Entry
Database: PDB / ID: 4zdk
TitleCrystal structure of the M. tuberculosis CTP synthase PyrG in complex with UTP, AMP-PCP and oxonorleucine
ComponentsCTP synthase
KeywordsLIGASE / CTP synthase / PyrG / amidotransferase / UTP / AMP-PCP / 5-oxo-L-norleucine
Function / homology
Function and homology information


CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / metal ion binding ...CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / P-loop containing nucleotide triphosphate hydrolases ...CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / 5-OXO-L-NORLEUCINE / URIDINE 5'-TRIPHOSPHATE / CTP synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsBellinzoni, M. / Barilone, N. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
European CommissionHEALTH-F3-2011-260872 France
CitationJournal: Chem.Biol. / Year: 2015
Title: Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG.
Authors: Mori, G. / Chiarelli, L.R. / Esposito, M. / Makarov, V. / Bellinzoni, M. / Hartkoorn, R.C. / Degiacomi, G. / Boldrin, F. / Ekins, S. / de Jesus Lopes Ribeiro, A.L. / Marino, L.B. / ...Authors: Mori, G. / Chiarelli, L.R. / Esposito, M. / Makarov, V. / Bellinzoni, M. / Hartkoorn, R.C. / Degiacomi, G. / Boldrin, F. / Ekins, S. / de Jesus Lopes Ribeiro, A.L. / Marino, L.B. / Centarova, I. / Svetlikova, Z. / Blasko, J. / Kazakova, E. / Lepioshkin, A. / Barilone, N. / Zanoni, G. / Porta, A. / Fondi, M. / Fani, R. / Baulard, A.R. / Mikusova, K. / Alzari, P.M. / Manganelli, R. / de Carvalho, L.P. / Riccardi, G. / Cole, S.T. / Pasca, M.R.
History
DepositionApr 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Jan 10, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CTP synthase
B: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,74510
Polymers127,4282
Non-polymers2,3188
Water00
1
B: CTP synthase
hetero molecules

A: CTP synthase
hetero molecules

B: CTP synthase
hetero molecules

A: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,49120
Polymers254,8564
Non-polymers4,63516
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
crystal symmetry operation6_645-x+1,-y-1/2,z1
crystal symmetry operation7_555-x+1/2,y,-z1
2
A: CTP synthase
hetero molecules

A: CTP synthase
hetero molecules

B: CTP synthase
hetero molecules

B: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,49120
Polymers254,8564
Non-polymers4,63516
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1/2,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
crystal symmetry operation7_555-x+1/2,y,-z1
Buried area16860 Å2
ΔGint-106 kcal/mol
Surface area72120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.732, 194.724, 207.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein CTP synthase / CTP synthetase / UTP--ammonia ligase


Mass: 63713.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: pyrG, Rv1699, MTCI125.21 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WHK7, CTP synthase (glutamine hydrolysing)
#2: Chemical ChemComp-ONL / 5-OXO-L-NORLEUCINE


Type: L-peptide linking / Mass: 145.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO3
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.84 Å3/Da / Density % sol: 74.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 30% PEG2000 MME, 100 mM bicine pH 9.0, 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 3.49→48.68 Å / Num. obs: 31727 / % possible obs: 99.6 % / Redundancy: 8.8 % / Biso Wilson estimate: 124.65 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.7
Reflection shellResolution: 3.49→3.67 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.128 / Mean I/σ(I) obs: 2.1 / % possible all: 98

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZDJ

4zdj


Resolution: 3.49→48.68 Å / Cor.coef. Fo:Fc: 0.9361 / Cor.coef. Fo:Fc free: 0.9403 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.937 / SU Rfree Blow DPI: 0.364
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 1598 5.04 %RANDOM
Rwork0.2028 ---
obs0.2034 31682 99.86 %-
Displacement parametersBiso mean: 143.24 Å2
Baniso -1Baniso -2Baniso -3
1-16.7546 Å20 Å20 Å2
2--12.7356 Å20 Å2
3----29.4902 Å2
Refine analyzeLuzzati coordinate error obs: 0.968 Å
Refinement stepCycle: LAST / Resolution: 3.49→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7844 0 142 0 7986
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088161HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0111169HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3623SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes168HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1280HARMONIC5
X-RAY DIFFRACTIONt_it8161HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion2.48
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1102SEMIHARMONIC5
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_contact9294SEMIHARMONIC4
LS refinement shellResolution: 3.49→3.6 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3039 139 4.83 %
Rwork0.2497 2740 -
all0.2522 2879 -
obs--99.86 %
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)
12.36910.2430.23372.39030.11732.0906-0.4307-0.2351-0.3053-0.1983-0.038-0.25490.18670.15770.4688-0.1254-0.16090.0104-0.14750.26250.099316.3374-40.6874-21.1395
24.85461.1190.83030.8666-2.00250.9013-0.0517-0.0840.0035-0.0345-0.0172-0.06350.06510.28710.06890.086-0.247-0.1338-0.04890.3040.158434.7802-25.2887-20.8782
32.4058-0.59450.3954.2179-1.04593.12250.11140.0156-0.1539-0.2951-0.1921-0.05750.0153-0.22180.0807-0.072-0.1003-0.0048-0.15810.11880.011317.6467-15.4654-45.2655
42.5093-0.735-0.36073.43130.06482.4727-0.05330.28550.59050.0239-0.2494-0.7796-0.21920.90530.3028-0.514-0.0288-0.21350.30590.21420.07669.7192-33.0392-6.6504
52.41493.94330.072.711-0.01710-0.00480.00450.0365-0.02360.0236-0.0386-0.03480.1119-0.0188-0.2096-0.295-0.27550.10710.17320.241376.7804-9.6511-6.3077
63.57-1.5910.96954.5855-2.01783.7350.13480.5310.5729-0.5517-0.3389-0.1518-0.39380.48870.204-0.3313-0.1855-0.0791-0.03410.3040.07357.1582-11.1595-30.6806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|7 - A|278 X|1 X|3 X|5 }
2X-RAY DIFFRACTION2{ A|279 - A|298 }
3X-RAY DIFFRACTION3{ A|299 - A|601 }
4X-RAY DIFFRACTION4{ B|7 - B|278 X|2 X|4 X|6 }
5X-RAY DIFFRACTION5{ B|279 - B|298 }
6X-RAY DIFFRACTION6{ B|299 - B|601 }

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