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- PDB-8tkb: tRNA 2-phosphotransferase (Tpt1) from Pyrococcus horikoshii in co... -

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Basic information

Entry
Database: PDB / ID: 8tkb
TitletRNA 2-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with 5'-AMP
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / 5'-AMP / AMP
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 MONOPHOSPHATE / : / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsJacewicz, A. / Dantuluri, S. / Shuman, S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-GM124165 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Other governmentHEI-S10OD021527 United States
CitationJournal: Rna / Year: 2025
Title: Structures of RNA phosphotransferase Tpt1 reveal distinct binding modes for an RNA 2'-PO 4 splice junction versus a 5'-PO 4 mononucleotide.
Authors: Jacewicz, A. / Damha, M.J. / Shuman, S.
History
DepositionJul 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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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)21,96115
Polymers20,8391
Non-polymers1,12214
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.937, 43.665, 122.861
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 / 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

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Non-polymers , 5 types, 93 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-Bicine (pH 8.3), 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 ...Details: 0.1 M Tris-Bicine (pH 8.3), 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: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.71→43.67 Å / Num. obs: 23319 / % possible obs: 99.4 % / Redundancy: 11.5 % / Biso Wilson estimate: 28.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.016 / Net I/σ(I): 23.5
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.114 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1195 / CC1/2: 0.837 / Rpim(I) all: 0.343 / % possible all: 99.5

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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: 1.71→41.14 Å / SU ML: 0.198 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7962
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2092 1151 4.95 %
Rwork0.1847 22110 -
obs0.1859 23261 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.53 Å2
Refinement stepCycle: LAST / Resolution: 1.71→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 58 79 1603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211562
X-RAY DIFFRACTIONf_angle_d1.21882110
X-RAY DIFFRACTIONf_chiral_restr0.0824225
X-RAY DIFFRACTIONf_plane_restr0.0119262
X-RAY DIFFRACTIONf_dihedral_angle_d7.6271248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.790.35211340.27772718X-RAY DIFFRACTION99.58
1.79-1.880.2431440.22042724X-RAY DIFFRACTION99.69
1.88-20.20621530.18962699X-RAY DIFFRACTION99.06
2-2.150.24151350.17962745X-RAY DIFFRACTION99.48
2.15-2.370.19811490.17572719X-RAY DIFFRACTION99.38
2.37-2.710.24651320.18682797X-RAY DIFFRACTION99.63
2.71-3.420.20061490.18542795X-RAY DIFFRACTION99.19
3.42-41.140.19181550.17682913X-RAY DIFFRACTION98.3
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)
13.664582265540.380303218352-1.024982431062.3862425322-0.826178019915.332070855830.04229731497870.0874105539199-0.02607543528440.0423959093906-0.03819406626860.0337456295466-0.07004506084250.096367379045-0.01077507609180.164880280745-0.00905738215425-0.02405897019180.1557383739470.01422719130170.1753068843726.2102832338714.449718680752.0441917118
23.586826899470.2524908538721.594367417273.853028602130.8858923527354.01063122778-0.0916538378562-0.04416039899270.100479958337-0.0764569889560.0898439725925-0.269435962906-0.1200958548040.1980647559740.00415907108510.184307825246-0.005713565623550.003363883597060.190159842172-0.02266878425990.2316252029917.403981021711.7761631079430.5095953399
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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