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- PDB-6tzm: Crystal Structure of Fungal RNA Kinase -

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Basic information

Entry
Database: PDB / ID: 6tzm
TitleCrystal Structure of Fungal RNA Kinase
ComponentstRNA ligase
KeywordsTRANSFERASE / RNA ligase / RNA repair / polynucleotide kinase
Function / homology
Function and homology information


GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / RNA ligase (ATP) / RNA ligase (ATP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / phosphoric diester hydrolase activity / endonuclease activity / phosphorylation / ATP binding / nucleus
Similarity search - Function
tRNA ligase Trl1, fungi / tRNA ligase, phosphodiesterase / tRNA ligase, kinase domain, fungi / Fungal tRNA ligase phosphodiesterase domain / tRNA ligase kinase domain / T4 RNA ligase 1, N-terminal / RNA ligase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / tRNA ligase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.714 Å
AuthorsShuman, S. / Goldgur, Y. / Banerjee, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM42498 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor.
Authors: Banerjee, A. / Goldgur, Y. / Schwer, B. / Shuman, S.
History
DepositionAug 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7013
Polymers50,2341
Non-polymers4682
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-17 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.562, 55.379, 81.419
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 tRNA ligase


Mass: 50233.672 Da / Num. of mol.: 1 / Fragment: UNP Residues 401-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876
Gene: LIG1, RLG1, TRL1, CAALFM_C702060WA, CaJ7.0238, CaO19.13864, CaO19.6511
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P43075, RNA ligase (ATP)
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsThe sequence conflicts are due to Candida having a special genetic code in which the leucine CUG ...The sequence conflicts are due to Candida having a special genetic code in which the leucine CUG codon is read as serine. Is is read as Leu in the expression system.

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 5, 30% PEG 6000- final pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 23506 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / CC1/2: 0.994 / Rpim(I) all: 0.035 / Net I/σ(I): 32
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 660 / CC1/2: 0.829 / Rpim(I) all: 0.227 / % possible all: 52

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 1.714→45.791 Å / σ(F): 1.36
RfactorNum. reflection% reflection
Rfree0.2091 3589 8.52 %
Rwork0.186 --
obs0.188 42100 88.83 %
Refinement stepCycle: LAST / Resolution: 1.714→45.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1729 0 29 157 1915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7145-1.7370.362640.3692695X-RAY DIFFRACTION41
1.737-1.76080.3965940.3509981X-RAY DIFFRACTION60
1.7608-1.7860.35051010.32351130X-RAY DIFFRACTION66
1.786-1.81260.34881180.29261281X-RAY DIFFRACTION77
1.8126-1.8410.3121260.25931371X-RAY DIFFRACTION84
1.841-1.87110.20691420.23771517X-RAY DIFFRACTION91
1.8711-1.90340.25131440.2161582X-RAY DIFFRACTION94
1.9034-1.9380.23991520.20631606X-RAY DIFFRACTION96
1.938-1.97530.22991560.20031615X-RAY DIFFRACTION96
1.9753-2.01560.21231560.20721599X-RAY DIFFRACTION97
2.0156-2.05940.20361520.19841599X-RAY DIFFRACTION96
2.0594-2.10740.21361430.20191588X-RAY DIFFRACTION95
2.1074-2.16010.21591370.19731484X-RAY DIFFRACTION90
2.1601-2.21850.26031450.20851620X-RAY DIFFRACTION95
2.2185-2.28370.21121500.17791575X-RAY DIFFRACTION95
2.2837-2.35740.19311440.18731589X-RAY DIFFRACTION96
2.3574-2.44170.25391500.18021586X-RAY DIFFRACTION95
2.4417-2.53950.21491450.18741571X-RAY DIFFRACTION95
2.5395-2.6550.21021450.17581601X-RAY DIFFRACTION94
2.655-2.7950.19881460.19421547X-RAY DIFFRACTION94
2.795-2.97010.22041470.18941533X-RAY DIFFRACTION92
2.9701-3.19930.21381390.18521463X-RAY DIFFRACTION88
3.1993-3.52120.23231420.17061584X-RAY DIFFRACTION95
3.5212-4.03040.181510.161562X-RAY DIFFRACTION94
4.0304-5.07690.15581490.14591625X-RAY DIFFRACTION97
5.0769-45.8070.1851510.1921607X-RAY DIFFRACTION97
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)
11.73730.322-0.02421.1154-0.65771.928-0.07950.01920.0194-0.09750.11920.1675-0.0122-0.19410.02580.15120.0005-0.01630.16460.01370.1716-45.32648.970691.9826
21.45240.6970.04211.9240.02640.9254-0.103-0.0620.04420.01690.08730.0275-0.00510.0168-0.00940.18750.0218-0.00720.16680.00240.135-39.293211.865799.8323
32.4126-0.4288-0.11536.5713-1.45862.43560.0734-0.23890.30090.0949-0.0088-0.2258-0.18130.13370.0150.2066-0.0018-0.01540.1863-0.05540.2146-35.464221.8044103.1416
42.07160.4219-0.47321.6766-0.91272.2942-0.04420.2642-0.0755-0.16650.0637-0.0820.16510.0528-0.0460.13250.01780.01480.1311-0.01210.1357-30.70166.011887.6139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 408 through 479 )
2X-RAY DIFFRACTION2chain 'A' and (resid 480 through 543 )
3X-RAY DIFFRACTION3chain 'A' and (resid 544 through 568 )
4X-RAY DIFFRACTION4chain 'A' and (resid 569 through 629 )

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