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- PDB-8tg4: tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in comple... -

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Basic information

Entry
Database: PDB / ID: 8tg4
TitletRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in complex with ADP-ribose-2"-phosphate and 2'-OH RNA
Components
  • Probable RNA 2'-phosphotransferase
  • RNA (5'-R(*UP*GP*UP*A)-3')
KeywordsTRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / ADP-ribose-2"-phosphate / Aeropyrum pernix
Function / homology
Function and homology information


tRNA 2'-phosphotransferase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / tRNA splicing, via endonucleolytic cleavage and ligation / NAD+-protein poly-ADP-ribosyltransferase activity
Similarity search - Function
RNA 2'-phosphotransferase KptA, putative / Phosphotransferase KptA/Tpt1 / RNA 2'-phosphotransferase, N-terminal domain / RNA 2'-phosphotransferase, C-terminal domain / RNA 2'-phosphotransferase, Tpt1 / KptA family
Similarity search - Domain/homology
Chem-9SO / : / NITRATE ION / RNA / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsJacewicz, A. / Dantuluri, S. / Shuman, S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Department of Energy (DOE, United States)DE-SC0012704 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-GM124165 United States
Other governmentHEI-S10OD021527 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD.
Authors: Jacewicz, A. / Dantuluri, S. / Shuman, S.
History
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable RNA 2'-phosphotransferase
C: RNA (5'-R(*UP*GP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,92111
Polymers24,9302
Non-polymers9919
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.844, 55.701, 42.249
Angle α, β, γ (deg.)90.000, 97.790, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / RNA chain , 2 types, 2 molecules AC

#1: Protein Probable RNA 2'-phosphotransferase


Mass: 23382.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: kptA, APE_0204.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon Plus
References: UniProt: Q9YFP5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: RNA chain RNA (5'-R(*UP*GP*UP*A)-3')


Mass: 1547.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 154 molecules

#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-9SO / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3R,4R,5R)-3,5-dihydroxy-4-(phosphonooxy)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 639.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N5O17P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.86 Å3/Da / Density % sol: 33.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M KNO3, 24% PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.37→41.86 Å / Num. obs: 38249 / % possible obs: 99.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 18.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Net I/σ(I): 22.4
Reflection shellResolution: 1.37→1.39 Å / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1848 / CC1/2: 0.741 / Rpim(I) all: 0.337

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wfx

1wfx


Resolution: 1.37→41.86 Å / SU ML: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4102
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.175 1935 5.06 %
Rwork0.1486 36296 -
obs0.1499 38231 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.04 Å2
Refinement stepCycle: LAST / Resolution: 1.37→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 48 54 145 1710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091607
X-RAY DIFFRACTIONf_angle_d1.21662193
X-RAY DIFFRACTIONf_chiral_restr0.0823241
X-RAY DIFFRACTIONf_plane_restr0.0184266
X-RAY DIFFRACTIONf_dihedral_angle_d14.1825242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.25271390.19872535X-RAY DIFFRACTION97.91
1.4-1.440.26371390.17662525X-RAY DIFFRACTION98.16
1.44-1.480.20551380.16142583X-RAY DIFFRACTION98.8
1.48-1.530.18911340.14272566X-RAY DIFFRACTION98.43
1.53-1.590.18961240.13962629X-RAY DIFFRACTION99.64
1.59-1.650.15671360.1342559X-RAY DIFFRACTION99.67
1.65-1.730.18661670.13362569X-RAY DIFFRACTION99.67
1.73-1.820.17321420.13252601X-RAY DIFFRACTION99.67
1.82-1.930.17621420.13132607X-RAY DIFFRACTION99.71
1.93-2.080.16631320.14382597X-RAY DIFFRACTION99.27
2.08-2.290.19091380.13922597X-RAY DIFFRACTION99.89
2.29-2.620.20421510.15882609X-RAY DIFFRACTION99.89
2.62-3.30.16511250.16212640X-RAY DIFFRACTION99.71
3.3-41.860.15151280.14572679X-RAY DIFFRACTION99.36

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