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- PDB-8tg5: tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in c... -

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Basic information

Entry
Database: PDB / ID: 8tg5
TitletRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with branched 2'-PO4 RNA
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / branched RNA / 2'-PO4 RNA
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
: / : / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-GM124165 United States
Department of Energy (DOE, United States)DE-SC0012704 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 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Jun 26, 2024Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year

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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)22,0297
Polymers20,8391
Non-polymers1,1906
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.291, 45.344, 125.239
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 / 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-9S2 / (2S,3R,4R,5S)-2-(6-amino-9H-purin-9-yl)-4-{[(S)-{[(2R,3S,4R,5S)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-({[(S)-{[(2R,3R,4S,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}(hydroxy)phosphoryl]oxy}methyl)oxolan-3-yl dihydrogen phosphate (non-preferred name)


Mass: 1005.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H38N15O19P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 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 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: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→45.34 Å / Num. obs: 15452 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 37.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.032 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.013 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1137 / CC1/2: 0.882 / Rpim(I) all: 0.314 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.64 Å / SU ML: 0.2769 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.573
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.243 766 4.98 %
Rwork0.1943 14619 -
obs0.1968 15385 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.84 Å2
Refinement stepCycle: LAST / Resolution: 2→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 72 62 1600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761589
X-RAY DIFFRACTIONf_angle_d0.93072155
X-RAY DIFFRACTIONf_chiral_restr0.0597228
X-RAY DIFFRACTIONf_plane_restr0.0094264
X-RAY DIFFRACTIONf_dihedral_angle_d12.3443214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.33641520.27932859X-RAY DIFFRACTION99.77
2.15-2.370.28961540.21922867X-RAY DIFFRACTION99.7
2.37-2.710.27161360.22462904X-RAY DIFFRACTION99.93
2.71-3.420.2551570.20572909X-RAY DIFFRACTION99.8
3.42-42.640.21361670.16763080X-RAY DIFFRACTION99.94
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)
14.95771176226-0.630038864383-0.3737536447693.784415106060.5774521619954.25625165241-0.07914082647490.351340791617-0.01325885514470.0150816769999-0.0505097368226-0.0639089968519-0.02380934194020.3853292601090.1116143514940.201827016588-0.0353438490162-0.008285858605380.2721669940620.01519608238020.2028257233255.9740472921914.353332100553.1895731512
24.11245310427-0.1426697602851.686344513683.257012729671.499751451686.20016726397-0.0219071181984-0.2097549700270.0795354436309-0.226506692952-0.1432065335370.043024973314-0.107988951952-0.01024370497190.1288816384510.3496264477710.006102320383970.03371221589850.290546930705-0.07366507789940.3750361201077.096391042380.90187307696731.679385709
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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