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- PDB-3syt: Crystal structure of glutamine-dependent NAD+ synthetase from M. ... -

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Basic information

Entry
Database: PDB / ID: 3syt
TitleCrystal structure of glutamine-dependent NAD+ synthetase from M. tuberculosis bound to AMP/PPi, NAD+, and glutamate
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 / NAD/GMP synthase / NAD synthase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily ...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 domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / 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 MONOPHOSPHATE / GLUTAMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYROPHOSPHATE 2- / Glutamine-dependent NAD(+) synthetase / Glutamine-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6511 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
DepositionJul 18, 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 1.2Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)304,94122
Polymers299,4224
Non-polymers5,51918
Water8,755486
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)609,88244
Polymers598,8438
Non-polymers11,03836
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area89690 Å2
ΔGint-275 kcal/mol
Surface area133420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.755, 177.755, 213.059
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 409:543 or resseq 557:679 )
211chain B and (resseq 1:402 or resseq 409:543 or resseq 557:679 )
311chain C and (resseq 1:402 or resseq 409:543 or resseq 557:679 )
411chain D and (resseq 1:402 or resseq 409:543 or resseq 557:679 )

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 74855.414 Da / Num. of mol.: 4
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)

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Non-polymers , 6 types, 504 molecules

#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 288 K / Method: evaporation / pH: 8
Details: 1.2 M ammonium citrate tribasic dihydrate, 5 % glycerol , pH 8.0, EVAPORATION, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / 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: 2.65→50 Å / Num. obs: 97718 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 8.2 % / Rsym value: 0.088 / Net I/σ(I): 20.4
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 9359 / Rsym value: 0.388 / % possible all: 95.8

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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: 2.6511→49.3 Å / SU ML: 0.65 / σ(F): 1.34 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2 4871 4.99 %RANDOM
Rwork0.1548 ---
obs0.1571 97557 98.51 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.351 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.5707 Å2-0 Å20 Å2
2---16.5707 Å20 Å2
3---33.1415 Å2
Refinement stepCycle: LAST / Resolution: 2.6511→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20193 0 356 486 21035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01521036
X-RAY DIFFRACTIONf_angle_d1.56128636
X-RAY DIFFRACTIONf_dihedral_angle_d16.3617569
X-RAY DIFFRACTIONf_chiral_restr0.093154
X-RAY DIFFRACTIONf_plane_restr0.0073716
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5066X-RAY DIFFRACTIONPOSITIONAL
12B5066X-RAY DIFFRACTIONPOSITIONAL0.092
13C4988X-RAY DIFFRACTIONPOSITIONAL0.11
14D5005X-RAY DIFFRACTIONPOSITIONAL0.086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6511-2.68120.31921500.25462851X-RAY DIFFRACTION93
2.6812-2.71270.27911550.22752970X-RAY DIFFRACTION96
2.7127-2.74580.33581570.2182992X-RAY DIFFRACTION96
2.7458-2.78050.27981560.21172977X-RAY DIFFRACTION96
2.7805-2.81710.22891590.19223000X-RAY DIFFRACTION97
2.8171-2.85570.28111580.19113026X-RAY DIFFRACTION97
2.8557-2.89650.26191560.20052969X-RAY DIFFRACTION97
2.8965-2.93970.25891570.19512962X-RAY DIFFRACTION96
2.9397-2.98570.27091570.19182994X-RAY DIFFRACTION96
2.9857-3.03460.25521570.19142997X-RAY DIFFRACTION97
3.0346-3.08690.27271620.1853091X-RAY DIFFRACTION99
3.0869-3.14310.25341620.17523085X-RAY DIFFRACTION100
3.1431-3.20350.24331630.16933094X-RAY DIFFRACTION100
3.2035-3.26890.23421640.16573134X-RAY DIFFRACTION100
3.2689-3.33990.18351650.15633118X-RAY DIFFRACTION100
3.3399-3.41760.20631630.15673111X-RAY DIFFRACTION100
3.4176-3.50310.21811630.16863111X-RAY DIFFRACTION100
3.5031-3.59770.1781650.1523123X-RAY DIFFRACTION100
3.5977-3.70360.18291640.14213141X-RAY DIFFRACTION100
3.7036-3.82310.1861640.13363116X-RAY DIFFRACTION100
3.8231-3.95970.16871650.13033136X-RAY DIFFRACTION100
3.9597-4.11810.15931640.11573130X-RAY DIFFRACTION100
4.1181-4.30540.15351650.10283128X-RAY DIFFRACTION100
4.3054-4.53230.13231650.10143161X-RAY DIFFRACTION100
4.5323-4.8160.15351670.10653159X-RAY DIFFRACTION100
4.816-5.18750.1581660.13073165X-RAY DIFFRACTION100
5.1875-5.70890.19371670.15923186X-RAY DIFFRACTION100
5.7089-6.53330.18671680.16353192X-RAY DIFFRACTION100
6.5333-8.22510.17391700.14833236X-RAY DIFFRACTION99
8.2251-49.30890.16481770.16243331X-RAY DIFFRACTION98
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)
10.71820.4634-0.00371.0052-0.05730.3544-0.04650.10270.0232-0.1902-0.04160.0671-0.0116-0.04390.0243-0.01650.0055-0.10310.0671-0.02130.0844-26.695817.4021-69.9299
20.3447-0.033-0.05110.66270.28130.4489-0.04920.00550.2903-0.0739-0.00590.1324-0.2138-0.06590.03820.14370.0427-0.07760.00990.00670.3278-15.813960.0461-56.7835
31.3548-0.303-0.06851.0974-0.03670.3571-0.01860.10730.0647-0.105-0.0256-0.0748-0.04440.03130.02820.0808-0.0208-0.01410.07510.01250.069916.962528.694-66.5255
40.6036-0.03930.33890.1762-0.03340.44650.00250.10350.11660.0024-0.0211-0.2472-0.04970.20720.03850.033-0.0235-0.0110.19860.00720.411459.641416.2477-54.8243
50.6729-0.24040.00370.89790.21740.3584-0.0224-0.12290.02170.1351-0.0449-0.09170.02190.04170.00530.0315-0.0169-0.0760.0943-0.01870.092526.265115.4001-34.5598
60.24620.0669-0.04640.7722-0.36550.6035-0.0303-0.06860.26150.1401-0.0274-0.1237-0.22690.11020.05280.1397-0.0509-0.06520.0756-0.07460.374915.453958.5572-42.696
71.35640.3840.12741.0019-0.0660.39780.0016-0.0796-0.15810.1309-0.0274-0.06820.06920.02160.02940.16280.0174-0.02050.07640.01620.163214.9916-28.3245-37.9982
80.8799-0.0567-0.59750.40370.04010.52720.0093-0.0946-0.16160.0443-0.038-0.33970.09810.22450.04530.15340.0488-0.08510.25230.01860.444858.2618-16.2916-44.5081
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 1:320)
6X-RAY DIFFRACTION6(chain D and resid 321:679)
7X-RAY DIFFRACTION7(chain C and resid 1:320)
8X-RAY DIFFRACTION8(chain C and resid 321:679)

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