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- PDB-3sez: Crystal structure of C176A mutant of glutamine-dependent NAD+ syn... -

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Basic information

Entry
Database: PDB / ID: 3sez
TitleCrystal structure of C176A mutant of glutamine-dependent NAD+ synthetase from M. tuberculosis in complex with ATP and NaAD+
ComponentsGlutamine-dependent NAD(+) synthetase
KeywordsLIGASE / Glutamine-amidotransferase / Glutaminase / Glutamine-dependent NAD+ synthetase / Ammonia tunneling / ATP binding / NAD / Nucleotide binding
Function / homology
Function and homology information


NAD+ synthase (glutamine-hydrolysing) / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / NAD+ biosynthetic process / glutaminase activity / peptidoglycan-based cell wall / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Glutamine-dependent NAD+ synthetase, C-terminal domain / Glutamine-dependent NAD+ synthetase, C-terminal / Glutamine-dependent NAD(+) synthetase / NAD(+) synthetase / NAD/GMP synthase / NAD synthase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase ...Glutamine-dependent NAD+ synthetase, C-terminal domain / Glutamine-dependent NAD+ synthetase, C-terminal / Glutamine-dependent NAD(+) synthetase / NAD(+) synthetase / NAD/GMP synthase / NAD synthase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / 4-Layer Sandwich / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / NICOTINIC ACID ADENINE DINUCLEOTIDE / Glutamine-dependent NAD(+) synthetase / Glutamine-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6529 Å
AuthorsChuenchor, W. / Gerratana, B.
CitationJournal: Biochem.J. / Year: 2012
Title: Regulation of the intersubunit ammonia tunnel in Mycobacterium tuberculosis glutamine-dependent NAD+ synthetase.
Authors: Chuenchor, W. / Doukov, T.I. / Resto, M. / Chang, A. / Gerratana, B.
History
DepositionJun 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_ref_seq_dif.details / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Sep 13, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Glutamine-dependent NAD(+) synthetase
B: Glutamine-dependent NAD(+) synthetase
C: Glutamine-dependent NAD(+) synthetase
D: Glutamine-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,98412
Polymers299,2934
Non-polymers4,6908
Water4,972276
1
A: Glutamine-dependent NAD(+) synthetase
B: Glutamine-dependent NAD(+) synthetase
C: Glutamine-dependent NAD(+) synthetase
D: Glutamine-dependent NAD(+) synthetase
hetero molecules

A: Glutamine-dependent NAD(+) synthetase
B: Glutamine-dependent NAD(+) synthetase
C: Glutamine-dependent NAD(+) synthetase
D: Glutamine-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)607,96824
Polymers598,5878
Non-polymers9,38116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area86460 Å2
ΔGint-241 kcal/mol
Surface area139430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.407, 178.407, 216.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:402 or resseq 409:541 or resseq 560:679 )
211chain B and (resseq 1:402 or resseq 409:541 or resseq 560:679 )
311chain C and (resseq 1:402 or resseq 409:541 or resseq 560:679 )
411chain D and (resseq 1:402 or resseq 409:541 or resseq 560:679 )

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Components

#1: Protein
Glutamine-dependent NAD(+) synthetase / NAD(+) synthase [glutamine-hydrolyzing]


Mass: 74823.352 Da / Num. of mol.: 4 / Mutation: C176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2513, MTCY428.08, nadE, Rv2438c / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A5L6, UniProt: P9WJJ3*PLUS, NAD+ synthase (glutamine-hydrolysing)
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N6O15P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 288 K / Method: evaporation / pH: 7.5
Details: 1.4 M ammonium citrate tribasic dihydrate, 10 % glycerol, pH 7.5, EVAPORATION, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 99130 / % possible obs: 98.1 % / Observed criterion σ(I): 1 / Redundancy: 14.2 % / Rsym value: 0.092 / Net I/σ(I): 27.4
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 9103 / Rsym value: 0.465 / % possible all: 91

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphenixphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DLA

3dla


Resolution: 2.6529→34.33 Å / SU ML: 0.7 / σ(F): 1.34 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 4936 4.99 %RANDOM
Rwork0.1725 ---
obs0.1746 98927 97.95 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.223 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--22.1463 Å2-0 Å20 Å2
2---22.1463 Å20 Å2
3---44.2926 Å2
Refinement stepCycle: LAST / Resolution: 2.6529→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20244 0 300 276 20820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01421043
X-RAY DIFFRACTIONf_angle_d1.53528650
X-RAY DIFFRACTIONf_dihedral_angle_d18.2587623
X-RAY DIFFRACTIONf_chiral_restr0.0933137
X-RAY DIFFRACTIONf_plane_restr0.0073731
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4997X-RAY DIFFRACTIONPOSITIONAL
12B4997X-RAY DIFFRACTIONPOSITIONAL0.085
13C4986X-RAY DIFFRACTIONPOSITIONAL0.079
14D5078X-RAY DIFFRACTIONPOSITIONAL0.085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6529-2.6830.31231440.29112759X-RAY DIFFRACTION88
2.683-2.71460.33131510.26812861X-RAY DIFFRACTION91
2.7146-2.74770.2961540.23642937X-RAY DIFFRACTION92
2.7477-2.78250.28851530.24122935X-RAY DIFFRACTION94
2.7825-2.81910.27171570.23132989X-RAY DIFFRACTION95
2.8191-2.85770.30451580.22773003X-RAY DIFFRACTION96
2.8577-2.89850.27981610.23463071X-RAY DIFFRACTION97
2.8985-2.94170.31581630.22113084X-RAY DIFFRACTION97
2.9417-2.98760.28021630.21413083X-RAY DIFFRACTION98
2.9876-3.03660.23931630.20923118X-RAY DIFFRACTION98
3.0366-3.08890.24711650.20423140X-RAY DIFFRACTION99
3.0889-3.14510.30471650.19583129X-RAY DIFFRACTION99
3.1451-3.20550.22451640.18383117X-RAY DIFFRACTION99
3.2055-3.27090.21131660.18523161X-RAY DIFFRACTION99
3.2709-3.34190.23831670.17563164X-RAY DIFFRACTION99
3.3419-3.41960.22491670.1813176X-RAY DIFFRACTION100
3.4196-3.50510.24541670.18443187X-RAY DIFFRACTION100
3.5051-3.59970.21781670.1663175X-RAY DIFFRACTION100
3.5997-3.70550.20371670.16173170X-RAY DIFFRACTION100
3.7055-3.8250.19361680.15593203X-RAY DIFFRACTION100
3.825-3.96150.18871670.15523173X-RAY DIFFRACTION100
3.9615-4.11990.21171680.14513201X-RAY DIFFRACTION100
4.1199-4.3070.14411670.12293202X-RAY DIFFRACTION100
4.307-4.53360.16111690.11993205X-RAY DIFFRACTION100
4.5336-4.8170.16941700.12683226X-RAY DIFFRACTION100
4.817-5.18770.1661680.13923218X-RAY DIFFRACTION100
5.1877-5.70760.2091720.17263261X-RAY DIFFRACTION100
5.7076-6.52860.21371710.18943265X-RAY DIFFRACTION100
6.5286-8.20680.19761740.16523317X-RAY DIFFRACTION100
8.2068-34.33260.17921800.17083461X-RAY DIFFRACTION100
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)
10.95530.32720.04931.2353-0.02110.3031-0.04690.1213-0.1299-0.1064-0.0124-0.14970.02580.02270.05340.27840.01210.07860.32010.01550.216126.9313-17.704737.3198
20.50990.00870.17941.0657-0.54990.6127-0.05050.0099-0.3744-0.0844-0.0353-0.25030.22330.13080.07230.40260.03470.09360.2795-0.01050.613116.0358-60.397250.6333
30.8968-0.1923-0.05751.0913-0.34650.3923-0.0009-0.1110.00440.0802-0.02920.1732-0.0102-0.01240.03190.3189-0.0190.0850.34590.00250.2495-26.0326-15.58572.91
40.48360.24760.06461.09960.37010.7862-0.0647-0.0719-0.32440.1669-0.03480.1710.2245-0.07820.08440.3521-0.03780.08370.28070.08120.5397-15.3172-58.852264.9287
51.4320.3849-0.12230.9632-0.05780.46240.0222-0.04640.2390.1444-0.03840.1777-0.0434-0.01530.01490.40170.02660.05670.2846-0.02420.3609-14.788528.176369.3454
61.2531-0.09650.62220.4819-0.21760.7856-0.0466-0.04480.37620.0516-0.05170.4696-0.1385-0.2250.0620.38860.05890.12610.4910.01510.8785-57.91516.459862.7917
71.2682-0.09650.02931.1435-0.09240.5907-0.03040.0957-0.1182-0.09730.00250.09220.0041-0.05440.03120.2898-0.02650.02250.2807-0.02730.2059-16.8087-28.968140.8997
80.80620.0432-0.38520.2853-0.1390.2729-0.05130.0333-0.15150.06430.00040.34470.0987-0.16010.06010.3315-0.03110.01940.5090.01690.7648-59.4799-16.609152.7457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:320)
2X-RAY DIFFRACTION2(chain A and resid 321:679)
3X-RAY DIFFRACTION3(chain B and resid 1:320)
4X-RAY DIFFRACTION4(chain B and resid 321:679)
5X-RAY DIFFRACTION5(chain C and resid 1:320)
6X-RAY DIFFRACTION6(chain C and resid 321:679)
7X-RAY DIFFRACTION7(chain D and resid :320)
8X-RAY DIFFRACTION8(chain D and resid 321:679)

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