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

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Basic information

Entry
Database: PDB / ID: 4zdj
TitleCrystal structure of the M. tuberculosis CTP synthase PyrG in complex with two UTP molecules
ComponentsCTP synthaseCTP synthetase
KeywordsLIGASE / CTP synthase / PyrG / amidotransferase / UTP
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 class-I / Glutamine amidotransferase / 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 class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / CTP synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8806
Polymers63,7711
Non-polymers1,1095
Water4,071226
1
A: CTP synthase
hetero molecules

A: CTP synthase
hetero molecules

A: CTP synthase
hetero molecules

A: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,52024
Polymers255,0844
Non-polymers4,43620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area20260 Å2
ΔGint-155 kcal/mol
Surface area71000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.410, 132.730, 157.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-908-

HOH

21A-925-

HOH

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Components

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


Mass: 63770.953 Da / Num. of mol.: 1
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-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 17% PEG20000, 100 mM MgCl2, 100 mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.99→48.9 Å / Num. obs: 56696 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 37.03 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.5
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.7 / % possible all: 92.9

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vcn

1vcn


Resolution: 1.99→39.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.9501 / SU R Cruickshank DPI: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.1889 2891 5.1 %RANDOM
Rwork0.1666 ---
obs0.1678 56691 98.78 %-
Displacement parametersBiso mean: 40.89 Å2
Baniso -1Baniso -2Baniso -3
1-4.9387 Å20 Å20 Å2
2---2.4312 Å20 Å2
3----2.5074 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: 1 / Resolution: 1.99→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4107 0 66 226 4399
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014266HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.975823HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1941SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes648HARMONIC5
X-RAY DIFFRACTIONt_it4266HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion2.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion558SEMIHARMONIC5
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_contact5227SEMIHARMONIC4
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2293 220 5.87 %
Rwork0.2106 3529 -
all0.2117 3749 -
obs--98.78 %
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)
10.63130.3578-0.16010.5169-0.1810.3605-0.05070.12990.0315-0.03390.0301-0.05360.02970.09270.0206-0.0460.0042-0.00130.00380.0359-0.046112.64859.831256.0467
24.3218-0.29250.21341.96640.8421.3504-0.02250.2997-0.0698-0.14820.037-0.2221-0.03460.3388-0.0145-0.0322-0.00880.0090.02310.038-0.014817.32718.849360.1005
32.7868-0.037-1.2623.57070.10050.2968-0.0242-0.0123-0.17540.0686-0.0345-0.22990.10690.12460.05880.01060.0182-0.0022-0.00710.0262-0.039216.2942-0.345367.0201
40.56460.232-0.12190.5836-0.33461.27940.0293-0.02740.10880.0957-0.0562-0.0933-0.16410.17320.0269-0.0427-0.0289-0.0219-0.03070.0292-0.025416.801920.66875.5494
53.26690.0860.46720.852-0.17411.319-0.02060.0260.49770.0888-0.01830.1516-0.2172-0.10320.0389-0.0670.0233-0.0105-0.10870.09850.04855.611938.721346.5231
63.2237-0.27750.45461.301-0.11541.0060.01590.64080.3284-0.1927-0.0320.0439-0.04890.03970.0161-0.1182-0.0129-0.00030.06170.168-0.092511.933631.228430.0307
71.8966-0.13120.58540.948-0.21260.7991-0.0650.22460.4394-0.00130.01670.0843-0.22840.19590.0484-0.0412-0.0503-0.0066-0.03180.13170.027917.044438.597144.6529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|5 - A|136 }
2X-RAY DIFFRACTION2{ A|137 - A|162 }
3X-RAY DIFFRACTION3{ A|163 - A|181 }
4X-RAY DIFFRACTION4{ A|182 - A|300 }
5X-RAY DIFFRACTION5{ A|301 - A|395 }
6X-RAY DIFFRACTION6{ A|396 - A|512 }
7X-RAY DIFFRACTION7{ A|513 - A|552 }

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