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- PDB-8tfi: tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 8tfi
TitletRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING
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
Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 11, 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)20,9103
Polymers20,8391
Non-polymers712
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.464, 44.807, 124.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 52.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1-0.3 M tris-bicine, 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, 8-14.8% PEG-8000
PH range: 8.3-8.5

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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: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.97→44.81 Å / Num. obs: 15955 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 38.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.025 / Net I/σ(I): 16.5
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2 / Num. unique obs: 1096 / CC1/2: 0.925 / Rpim(I) all: 0.297 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→42.17 Å / SU ML: 0.2126 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.2125
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2282 765 4.82 %
Rwork0.1932 15120 -
obs0.1948 15885 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.89 Å2
Refinement stepCycle: LAST / Resolution: 1.97→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 2 74 1541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891499
X-RAY DIFFRACTIONf_angle_d0.9512015
X-RAY DIFFRACTIONf_chiral_restr0.0641214
X-RAY DIFFRACTIONf_plane_restr0.0106256
X-RAY DIFFRACTIONf_dihedral_angle_d5.7868206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.120.29371600.25092951X-RAY DIFFRACTION99.68
2.12-2.340.26541560.21512938X-RAY DIFFRACTION99.77
2.34-2.670.24381510.19943008X-RAY DIFFRACTION99.97
2.67-3.370.27571350.21853039X-RAY DIFFRACTION99.75
3.37-42.170.19671630.17243184X-RAY DIFFRACTION99.85
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)
16.10121760593-0.516173404804-2.012204424253.941502457660.396460569767.21740415309-0.01079499721430.2278398675730.016528758306-0.00626626541049-0.0234234579717-0.0554192773091-0.1207087349240.182826601470.03128855707220.241781327704-0.0415695996718-0.02774258727780.3249587160130.02555042645390.2063905892245.8659930196414.109701694252.7502299593
26.823468939661.405749553255.690109857655.149803371492.909090939897.64641729301-0.193809176896-0.3065361513380.212794395614-0.3218900652190.0808288920111-0.0547793062195-0.0772463471504-0.09469746419210.0697641542740.351107257253-0.001180370848430.07725046258110.368294991412-0.02280466606980.3157043432037.675894399530.54267988486830.323524831
31.353568485-2.128054283570.3093998146366.432433039421.294420548321.243635289950.0025678358569-0.2253368941140.882911889810.848478969446-0.137543866634-0.562001925266-1.208467822760.412063216797-0.02946145141940.588877473956-0.0517264939309-0.0215884872120.586948032192-0.03726355029650.599076187568.59207713756.3288514150433.2523747721
48.263932742871.052288701366.304919381384.920861065380.3131324389627.149909856230.0642399071199-0.09365017573980.0658808420975-0.0194927907905-0.0779016079377-0.008064378103480.21083421152-0.09996422476760.0523034947150.388214972831-0.01224846161270.03564186007950.375963833384-0.04312957699390.253335506766.50371087178-0.99849520504432.0557394123
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 82 )1 - 821 - 82
22chain 'A' and (resid 83 through 108 )83 - 10883 - 108
33chain 'A' and (resid 109 through 123 )109 - 123109 - 123
44chain 'A' and (resid 124 through 177 )124 - 177124 - 177

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