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- PDB-9dsq: Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) ... -

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Basic information

Entry
Database: PDB / ID: 9dsq
TitleThermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with products TC-AMP and pyrophosphate
ComponentsThreonylcarbamoyl-AMP synthase
KeywordsBIOSYNTHETIC PROTEIN / TsaC2 / TsaC / t6A / N6-threonylcarbamoyl adenosine / t6A37 / tRNA / transfer-RNA / reaction intermediate / TC-AMP
Function / homology
Function and homology information


L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA processing / regulation of translational fidelity / nucleotidyltransferase activity / double-stranded RNA binding / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
tRNA threonylcarbamoyladenosine biosynthesis protein SUA5 / Threonylcarbamoyl-AMP synthase, C-terminal domain / Threonylcarbamoyl-AMP synthase, C-terminal domain superfamily / Threonylcarbamoyl-AMP synthase, C-terminal domain / : / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination / YrdC-like domain profile. / DHBP synthase RibB-like alpha/beta domain superfamily
Similarity search - Domain/homology
ACETATE ION / DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / threonylcarbamoyladenylate / Threonylcarbamoyl-AMP synthase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.99 Å
AuthorsKutshuashvili, A. / Swairjo, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110588 United States
CitationJournal: To Be Published
Title: Crystallographic evidence of N-carboxy-L-threonine intermediate in t6A modification of tRNA.
Authors: Kutchaushvili, A. / Wood, E. / Luthra, A. / Hung, S.-H. / Swinehart, W. / Bayooz, S. / Scheleen, E. / Iwata-Reuyl, D. / Swairjo, M.A.
History
DepositionSep 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Threonylcarbamoyl-AMP synthase
B: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,56414
Polymers76,7162
Non-polymers1,84912
Water3,747208
1
A: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1676
Polymers38,3581
Non-polymers8095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3988
Polymers38,3581
Non-polymers1,0407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.825, 153.825, 86.892
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-635-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Threonylcarbamoyl-AMP synthase / TC-AMP synthase / L-threonylcarbamoyladenylate synthase


Mass: 38357.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal 5 residues (GSHMA) are left from thrombin cutting site after removal of an N-terminal His6 tag.
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: ATCC 43589 / Gene: TM_0852 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9WZV6, L-threonylcarbamoyladenylate synthase

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Non-polymers , 7 types, 220 molecules

#2: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TXA / threonylcarbamoyladenylate


Mass: 492.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N6O11P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.87 Å3/Da / Density % sol: 68.27 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion / pH: 7.4
Details: Reservoir solution: 500 ul 80 mM sodium cacodylate, pH 7.4, 0.23 M sodium acetate, 13.5% PEG8000, 20% glycerol. Protein: 25 mg/mL TmTsaC2, 50 mM Tris, pH 7.5, 50 mM KCl, 1 mM DTT, 10 mM L- ...Details: Reservoir solution: 500 ul 80 mM sodium cacodylate, pH 7.4, 0.23 M sodium acetate, 13.5% PEG8000, 20% glycerol. Protein: 25 mg/mL TmTsaC2, 50 mM Tris, pH 7.5, 50 mM KCl, 1 mM DTT, 10 mM L-threonine, 30 mM sodium bicarbonate. Crystal soaked in 14% PEG8000, 20% glycerol, 0.2 M sodium acetate, 80 mM sodium cacodylate, pH 7.4, 10 mM L-threonine, 10 mM ATP, 10 mM MgCl2, 30 mM bicarbonate, 0.11 u/ul inorganic pyrophosphatase

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.99→44.44 Å / Num. obs: 81174 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 18.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.064 / Rrim(I) all: 0.279 / Net I/σ(I): 7.9
Reflection shellResolution: 1.99→2.03 Å / Rmerge(I) obs: 5.124 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4420 / CC1/2: 0.322 / Rpim(I) all: 1.197 / Rrim(I) all: 5.263 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
pointless1.12.10data scaling
REFMAC5.8.0258phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.99→44.44 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.349 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 4176 5.1 %RANDOM
Rwork0.19695 ---
obs0.19828 76961 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.036 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å2-0 Å2
3----3.17 Å2
Refinement stepCycle: 1 / Resolution: 1.99→44.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5123 0 117 208 5448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125466
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165460
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.8587436
X-RAY DIFFRACTIONr_angle_other_deg0.4321.7612665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.156536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79210993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2863
X-RAY DIFFRACTIONr_gen_planes_refined00.026109
X-RAY DIFFRACTIONr_gen_planes_other00.021081
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1874.5992636
X-RAY DIFFRACTIONr_mcbond_other4.1724.5982635
X-RAY DIFFRACTIONr_mcangle_it6.018.2533303
X-RAY DIFFRACTIONr_mcangle_other6.018.2543304
X-RAY DIFFRACTIONr_scbond_it5.4925.2572830
X-RAY DIFFRACTIONr_scbond_other5.4915.2582831
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2849.3654128
X-RAY DIFFRACTIONr_long_range_B_refined10.29944.495836
X-RAY DIFFRACTIONr_long_range_B_other10.29444.095806
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 302 -
Rwork0.365 5605 -
obs--99.95 %

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