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- PDB-1fhq: REFINED SOLUTION STRUCTURE OF THE FHA2 DOMAIN OF RAD53 -

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Entry
Database: PDB / ID: 1fhq
TitleREFINED SOLUTION STRUCTURE OF THE FHA2 DOMAIN OF RAD53
ComponentsPROTEIN KINASE SPK1
KeywordsTRANSFERASE / FHA domain / Rad53 / Phosphotyrosine / Phosphoprotein
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / dual-specificity kinase / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling ...deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / dual-specificity kinase / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / intracellular protein localization / protein tyrosine kinase activity / protein kinase activity / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase Rad53 / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Aurora kinase / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site ...Serine/threonine-protein kinase Rad53 / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Aurora kinase / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase RAD53
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsByeon, I.-J.L. / Liao, H. / Tsai, M.-D.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: II. Structure and specificity of the interaction between the FHA2 domain of Rad53 and phosphotyrosyl peptides.
Authors: Wang, P. / Byeon, I.J. / Liao, H. / Beebe, K.D. / Yongkiettrakul, S. / Pei, D. / Tsai, M.D.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Structure and Function of a New Phosphopeptide-Binding Domain Containing the FHA2 of Rad53
Authors: Liao, H. / Byeon, I.-J.L. / Tsai, M.-D.
History
DepositionAug 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN KINASE SPK1


Theoretical massNumber of molelcules
Total (without water)18,1491
Polymers18,1491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with the lowest energy
RepresentativeModel #20minimized average structure

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Components

#1: Protein PROTEIN KINASE SPK1


Mass: 18148.758 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FHA DOMAIN (FHA2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PGEX-4T / Production host: Escherichia coli (E. coli)
References: UniProt: P22216, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.5 mM protein U-15N,13C; 10 mM sodium phosphate buffer (pH 6.5), 1 mM DTT, and 1 mM EDTA; 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 10 mM sodium phosphate, 1 mM DTT, and 1 mM EDTA
pH: 6.5 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 3249 restraints, 3061 are NOE-derived distance constraints, 188 TALOS-derived dihedral angle restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20

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