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

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Basic information

Entry
Database: PDB / ID: 3seq
TitleCrystal structure of C176A mutant of glutamine-dependent NAD+ synthetase from M. tuberculosis in complex with AMPCPP 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 / glutaminase activity / NAD biosynthetic process / 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 / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / NAD/GMP synthase / NAD synthase / 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 / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / NAD/GMP synthase / NAD synthase / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / 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: 2.7342 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 10, 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)304,16014
Polymers299,2934
Non-polymers4,86710
Water6,287349
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)608,32028
Polymers598,5878
Non-polymers9,73320
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area87060 Å2
ΔGint-249 kcal/mol
Surface area136310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.166, 178.166, 214.907
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 0:401 or resseq 409:441 or resseq 453:542 or resseq 561:679 )
211chain B and (resseq 0:401 or resseq 410:441 or resseq 453:542 or resseq 561:679 )
311chain C and (resseq 0:401 or resseq 409:441 or resseq 453:542 or resseq 561:679 )
411chain D and (resseq 0:401 or resseq 409:441 or resseq 453:542 or resseq 561:679 )

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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-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 288 K / Method: evaporation / pH: 8
Details: 1.4 M ammonium citrate tribasic dihydrate, 7.5 % glycerol, pH 8.0, EVAPORATION, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.734→50 Å / Num. obs: 88274 / % possible obs: 96.6 % / Observed criterion σ(I): 1 / Redundancy: 14.5 % / Rsym value: 0.171 / Net I/σ(I): 15.6
Reflection shellResolution: 2.734→2.85 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.549 / % possible all: 91.2

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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: 2.7342→40.091 Å / SU ML: 0.9 / Isotropic thermal model: Anisotropic / σ(F): 1.34 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 4398 4.99 %
Rwork0.1626 --
obs0.1652 88156 96.27 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.492 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.4962 Å2-0 Å20 Å2
2---5.4962 Å20 Å2
3---41.4724 Å2
Refinement stepCycle: LAST / Resolution: 2.7342→40.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20159 0 312 349 20820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01220965
X-RAY DIFFRACTIONf_angle_d1.4728554
X-RAY DIFFRACTIONf_dihedral_angle_d17.2987533
X-RAY DIFFRACTIONf_chiral_restr0.0873149
X-RAY DIFFRACTIONf_plane_restr0.0063703
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4935X-RAY DIFFRACTIONPOSITIONAL
12B4935X-RAY DIFFRACTIONPOSITIONAL0.065
13C4941X-RAY DIFFRACTIONPOSITIONAL0.071
14D4938X-RAY DIFFRACTIONPOSITIONAL0.067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7342-2.83190.36093970.28197569X-RAY DIFFRACTION88
2.8319-2.94520.30184320.22818223X-RAY DIFFRACTION96
2.9452-3.07920.27644420.19678414X-RAY DIFFRACTION98
3.0792-3.24150.25554440.18288466X-RAY DIFFRACTION99
3.2415-3.44450.21794470.17088510X-RAY DIFFRACTION99
3.4445-3.71020.2164470.15888497X-RAY DIFFRACTION98
3.7102-4.08330.17274450.13358496X-RAY DIFFRACTION98
4.0833-4.67340.15244480.11798523X-RAY DIFFRACTION98
4.6734-5.8850.21184470.15538508X-RAY DIFFRACTION97
5.885-40.09560.1794490.15448552X-RAY DIFFRACTION93
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)
10.32570.20040.03690.47760.0190.2347-0.05640.0808-0.0225-0.0524-0.0296-0.0721-0.00660.03430.00880.0480.01490.09750.06160.02450.032726.7768-17.604336.9414
20.3202-0.01950.01730.4689-0.12580.365-0.0478-0.0065-0.2782-0.0498-0.025-0.13030.22850.05570.01460.07730.08060.0821-0.1057-0.02790.253515.929-60.216250.2453
30.544-0.16930.00610.4781-0.02760.3946-0.03380.0925-0.0562-0.1057-0.00830.0470.0334-0.04740.02120.0834-0.03410.01970.0939-0.02710.0213-16.8899-28.851740.4595
40.3747-0.0224-0.14080.17690.01530.3131-0.02950.0474-0.10430.025-0.00540.23630.0599-0.19330.034-0.0055-0.06290.01160.22430.02190.3615-59.5088-16.401852.3221
50.256-0.0681-0.06570.3529-0.08120.2888-0.027-0.07990.00310.0814-0.03130.0867-0.0525-0.0678-0.0467-0.0509-0.07730.1370.07620.0372-0.0265-26.1297-15.560772.6107
60.16860.0538-0.03620.52410.13390.4484-0.0485-0.0011-0.2530.0666-0.02830.11650.1877-0.09710.03970.1084-0.08220.08050.06050.11130.3008-15.3755-58.727764.3496
70.73240.1491-0.16110.59460.03760.3760.0129-0.02930.08940.1547-0.06570.0934-0.0249-0.06750.04570.14110.01020.03580.0638-0.02280.1168-14.939528.229369.1068
80.63810.01910.34180.30250.04340.4554-0.0117-0.05910.2190.0122-0.03070.3137-0.0843-0.19370.02530.11040.03130.09960.2076-0.00140.4508-58.127416.338162.4108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:320)
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 D and resid 0:320)
6X-RAY DIFFRACTION6(chain D and resid 321:679)
7X-RAY DIFFRACTION7(chain C and resid 0:320)
8X-RAY DIFFRACTION8(chain C and resid 321:679)

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