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

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Basic information

Entry
Database: PDB / ID: 8tfx
TitletRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with 2',5'-ADP
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / 2' / 5'-ADP
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+ 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
ADENOSINE-2'-5'-DIPHOSPHATE / : / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,03617
Polymers20,8391
Non-polymers1,19716
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.554, 44.626, 124.397
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

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Protein , 1 types, 1 molecules A

#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): (DE3) Codon Plus
References: UniProt: O57899, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Non-polymers , 6 types, 131 molecules

#2: Chemical ChemComp-A2P / ADENOSINE-2'-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
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
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: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→44.63 Å / Num. obs: 24459 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 26.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.016 / Net I/σ(I): 25.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1269 / CC1/2: 0.918 / Rpim(I) all: 0.223 / % possible all: 99.9

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Processing

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

8tfi


Resolution: 1.7→42 Å / SU ML: 0.2167 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2032 1218 4.99 %
Rwork0.1762 23173 -
obs0.1775 24391 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.65 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 65 115 1646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01431567
X-RAY DIFFRACTIONf_angle_d1.4672102
X-RAY DIFFRACTIONf_chiral_restr0.0943220
X-RAY DIFFRACTIONf_plane_restr0.0152262
X-RAY DIFFRACTIONf_dihedral_angle_d7.5914220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.36561280.30032523X-RAY DIFFRACTION99.85
1.77-1.850.24891400.22122527X-RAY DIFFRACTION99.74
1.85-1.950.23171460.17932527X-RAY DIFFRACTION99.96
1.95-2.070.22711280.18472522X-RAY DIFFRACTION99.89
2.07-2.230.25891250.1782570X-RAY DIFFRACTION100
2.23-2.450.19871400.18042546X-RAY DIFFRACTION99.96
2.45-2.810.21951220.1832600X-RAY DIFFRACTION99.74
2.81-3.530.21261370.17312609X-RAY DIFFRACTION100
3.54-420.16441520.15932749X-RAY DIFFRACTION99.93
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)
13.384655113390.0486724150592-0.9788774021042.574818765670.06093706656624.15774961809-0.01364113280180.003310074591870.07035742531630.04917635997370.003110666794860.00599063637376-0.1048290835430.1311103779930.01710701983040.147357984762-0.0156448247522-0.01732199678930.1381469967750.004044340691610.1368808897755.9774489039414.152007701752.6879461526
23.2794958394-0.1808376357392.017207548312.911427280211.330340091444.10634243304-0.0831451550795-0.02255694916550.104019891487-0.1647607483640.00606216931367-0.0808003775451-0.09223271605650.1389183050330.0499727769080.225139887526-0.008969779278010.03204984568470.168377577734-0.01766472759150.235458126946.816430069230.8233647252531.5991411314
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 177 )83 - 17783 - 177

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