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- PDB-9d3h: Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) ... -

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Basic information

Entry
Database: PDB / ID: 9d3h
TitleThermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with N-carboxy-L-threonine, magnesium 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 activity / 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 / N-carboxy-L-threonine / Threonylcarbamoyl-AMP synthase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.28 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
DepositionAug 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,76722
Polymers76,7162
Non-polymers2,05120
Water2,720151
1
A: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1207
Polymers38,3581
Non-polymers7626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Threonylcarbamoyl-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,64715
Polymers38,3581
Non-polymers1,28914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.039, 154.039, 87.241
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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 , 8 types, 171 molecules

#2: Chemical ChemComp-U6A / N-carboxy-L-threonine


Type: L-peptide NH3 amino terminus / Mass: 163.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion / pH: 7.4
Details: Reservoir solution: 500 ul 80 mM sodium cacodylate, pH 7.4, 0.15 M sodium acetate, 14.3% 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, 0.15 M sodium acetate, 14.3% PEG8000, 20% glycerol Protein: 25 mg/mL TmTsaC2, 50 mM Tris, pH 7.5, 50 mM KCl, 1 mM DTT, 10 mM L-threonine, 10 mM ATP, 10 mM MgCl2, 30 mM sodium acetate; protein was preheated at 60 C for 30 mins drop is 1.5 ul reservoir + 1.5 ul sample.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 4, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 2.277→34.09 Å / Num. obs: 54251 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 12.8 % / CC1/2: 0.3 / Rmerge(I) obs: 0.374 / Rpim(I) all: 0.108 / Rrim(I) all: 0.39 / Net I/σ(I): 7.7
Reflection shellResolution: 2.277→2.317 Å / Rmerge(I) obs: 3.685 / Num. unique obs: 2696 / CC1/2: 0.419 / Rpim(I) all: 1.06 / Rrim(I) all: 3.836 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
pointless1.12.10data scaling
REFMAC5.8.0258phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.28→34.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.876 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21246 2724 5 %RANDOM
Rwork0.18747 ---
obs0.18873 51476 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.005 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.28→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5343 0 130 151 5624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135629
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175590
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6597611
X-RAY DIFFRACTIONr_angle_other_deg1.181.58312990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2485681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78721.787263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.684151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5511537
X-RAY DIFFRACTIONr_chiral_restr0.0740.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.026059
X-RAY DIFFRACTIONr_gen_planes_other00.021084
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_it1.0712.6442714
X-RAY DIFFRACTIONr_mcbond_other1.0512.6362708
X-RAY DIFFRACTIONr_mcangle_it1.763.9523392
X-RAY DIFFRACTIONr_mcangle_other1.7613.9533393
X-RAY DIFFRACTIONr_scbond_it1.4812.9442915
X-RAY DIFFRACTIONr_scbond_other1.482.9462916
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4054.2914219
X-RAY DIFFRACTIONr_long_range_B_refined4.84831.2535766
X-RAY DIFFRACTIONr_long_range_B_other4.84831.2645767
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.336 Å
RfactorNum. reflection% reflection
Rfree0.338 185 -
Rwork0.309 3785 -
obs--98.83 %
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)
11.7604-0.2376-0.13231.96440.21273.8196-0.019-0.2009-0.05830.2360.05930.2110.3546-0.3889-0.04030.20370.03910.02210.14940.01050.0672-98.759428.4163-0.0843
20.75520.20540.1552.84050.29432.5301-0.03250.1150.1114-0.23970.0741-0.0959-0.25310.1605-0.04160.1662-0.00040.0110.03240.01280.0234-68.314619.2807-20.7666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 404
2X-RAY DIFFRACTION2B0 - 404

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