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- PDB-1k2m: Solution Structure of the FHA2 Domain of Rad53 Complexed with a P... -

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Basic information

Entry
Database: PDB / ID: 1k2m
TitleSolution Structure of the FHA2 Domain of Rad53 Complexed with a Phosphotyrosyl Peptide Derived from Rad9
Components
  • DNA repair protein Rad9
  • Protein Kinase SPK1
KeywordsTRANSFERASE / FHA domain / Rad53 / Rad9 / Phosphotyrosine / phosphoprotein
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / negative regulation of DNA strand resection involved in replication fork processing / meiotic recombination checkpoint signaling / SUMOylation of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / dual-specificity kinase / mitotic intra-S DNA damage checkpoint signaling / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding ...deoxyribonucleoside triphosphate biosynthetic process / negative regulation of DNA strand resection involved in replication fork processing / meiotic recombination checkpoint signaling / SUMOylation of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / dual-specificity kinase / mitotic intra-S DNA damage checkpoint signaling / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding / DNA replication initiation / regulation of DNA repair / mitotic G1 DNA damage checkpoint signaling / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / nucleotide-excision repair / enzyme activator activity / intracellular protein localization / double-strand break repair / double-stranded DNA binding / protein tyrosine kinase activity / histone binding / protein kinase activity / regulation of cell cycle / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / chromatin / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Rad9-like Rad53-binding domain, fungi / Fungal Rad9-like Rad53-binding / Serine/threonine-protein kinase Rad53 / : / : / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Aurora kinase / Forkhead associated domain / Forkhead-associated (FHA) domain profile. ...Rad9-like Rad53-binding domain, fungi / Fungal Rad9-like Rad53-binding / 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 / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT 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
DNA repair protein RAD9 / Serine/threonine-protein kinase RAD53
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsByeon, I.-J.L. / Yongkiettrakul, S. / Tsai, M.-D.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Solution structure of the yeast Rad53 FHA2 complexed with a phosphothreonine peptide pTXXL: comparison with the structures of FHA2-pYXL and FHA1-pTXXD complexes.
Authors: Byeon, I.J. / Yongkiettrakul, S. / Tsai, M.D.
#1: 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.
#2: 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. / Tsai, M.D.
History
DepositionSep 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Kinase SPK1
P: DNA repair protein Rad9


Theoretical massNumber of molelcules
Total (without water)19,1592
Polymers19,1592
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)22 / 100structures with the lowest energy
Representative

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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)
Gene: SPK1 or RAD53 / Plasmid: pGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P22216, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein/peptide DNA repair protein Rad9


Mass: 1009.947 Da / Num. of mol.: 1 / Fragment: residues 826-832 / Source method: obtained synthetically
Details: This phosphotyrosyl peptide was chemically synthesized.
References: UniProt: P14737
Has protein modificationY

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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 FHA2 U-15N,13C; 1mM phosphotyrosyl peptide of Rad9; 10 mM sodium phosphate (pH 6.5), 1 mM DTT, and 1 mM EDTA
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 10 mM sodium phosphate(pH 6.5), 1 mM DTT, and 1 mM EDTA
pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
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 complex structures are generated using a total of 3398 restraints, 3210 distance restraints, and 188 TOLOS-derived dihedral angle restraints.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 22

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