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- PDB-8tfy: tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in c... -

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Basic information

Entry
Database: PDB / ID: 8tfy
TitletRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with NADP
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / NADP / NAD
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / tRNA splicing, via endonucleolytic cleavage and ligation / NAD+ 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsJacewicz, A. / Dantuluri, S. / Shuman, S.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
National Institutes of Health/Office of the DirectorS10OD030394 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6544
Polymers20,8391
Non-polymers8143
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.671, 44.531, 124.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Probable RNA 2'-phosphotransferase


Mass: 20839.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: kptA, PH0160 / Plasmid: pET28b-His10Smt3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon Plus
References: UniProt: O57899, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1-0.3 M Tris-Bicine (pH 8.3 or 8.5), 0.1 M amino acid additives mixture (0.02 M each of DL-glutamic acid monohydrate, DL-alanine, glycine, DL-lysine monohydrate and DL-serine), 16-29.6% ...Details: 0.1-0.3 M Tris-Bicine (pH 8.3 or 8.5), 0.1 M amino acid additives mixture (0.02 M each of DL-glutamic acid monohydrate, DL-alanine, glycine, DL-lysine monohydrate and DL-serine), 16-29.6% ethylene glycol, and 8-14.8% PEG-8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 33140 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 20.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.024 / Net I/σ(I): 42.5
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.005 / Num. unique obs: 1611 / CC1/2: 0.807 / Rpim(I) all: 0.398 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8TFI

8tfi


Resolution: 1.54→29.2 Å / SU ML: 0.142 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.271
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.193 1603 4.94 %
Rwork0.17 --
obs0.172 32431 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.53 Å2
Refinement stepCycle: LAST / Resolution: 1.54→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 33 103 1602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081543
X-RAY DIFFRACTIONf_angle_d0.9682085
X-RAY DIFFRACTIONf_dihedral_angle_d8.836232
X-RAY DIFFRACTIONf_chiral_restr0.063223
X-RAY DIFFRACTIONf_plane_restr0.011260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.590.26971420.2142688X-RAY DIFFRACTION97
1.59-1.650.231410.16982701X-RAY DIFFRACTION98
1.65-1.710.19411400.1582736X-RAY DIFFRACTION98
1.71-1.790.20831450.16342759X-RAY DIFFRACTION98
1.79-1.880.23471430.15832750X-RAY DIFFRACTION99
1.88-20.17831390.15162800X-RAY DIFFRACTION100
2-2.160.18431490.15252821X-RAY DIFFRACTION100
2.16-2.370.22291500.16882810X-RAY DIFFRACTION100
2.37-2.720.18791330.17732866X-RAY DIFFRACTION100
2.72-3.420.18721590.18042876X-RAY DIFFRACTION100
3.42-29.20.1791620.17143021X-RAY DIFFRACTION100

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