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(-) Description

Title :  SOLUTION STRUCTURE OF THE FHA2 DOMAIN OF RAD53 COMPLEXED WITH A PHOSPHOTHREONYL PEPTIDE DERIVED FROM RAD9
 
Authors :  I. -J. L. Byeon, S. Yongkiettrakul, M. -D. Tsai
Date :  03 Oct 01  (Deposition) - 05 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,P
Keywords :  Fha Domain, Rad53, Rad9, Phosphothreonine, Phosphoprotein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. J. Byeon, S. Yongkiettrakul, M. D. Tsai
Solution Structure Of The Yeast Rad53 Fha2 Complexed With A Phosphothreonine Peptide Ptxxl: Comparison With The Structures Of Fha2-Pyxl And Fha1-Ptxxd Complexes.
J. Mol. Biol. V. 314 577 2001
PubMed-ID: 11846568  |  Reference-DOI: 10.1006/JMBI.2001.5141
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN KINASE SPK1
    ChainsA
    EC Number2.7.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-4T
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL FHA DOMAIN (FHA2)
    GeneSPK1 OR RAD53
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
 
Molecule 2 - DNA REPAIR PROTEIN RAD9
    ChainsP
    EngineeredYES
    FragmentRESIDUES 599-607
    Other DetailsTHIS PHOSPHOTHREONYL PEPTIDE WAS CHEMICALLY SYNTHESIZED.
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (0, 0)

(no "Site" information available for 1J4L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J4L)

(-) Cis Peptide Bonds  (1, 1)

NMR Structure
No.Residues
1Asn A:599 -Pro A:600

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J4L)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FHA_DOMAINPS50006 Forkhead-associated (FHA) domain profile.RAD53_YEAST66-116
601-664
  1-
A:601-664

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR217C1YDR217C.1IV:903477-8995483930RAD9_YEAST1-130913091P:599-6079

2.1YPL153C1YPL153C.1XVI:264191-2617262466RAD53_YEAST1-8218211A:573-730158

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:158
 aligned with RAD53_YEAST | P22216 from UniProtKB/Swiss-Prot  Length:821

    Alignment length:158
                                   582       592       602       612       622       632       642       652       662       672       682       692       702       712       722        
          RAD53_YEAST   573 GNGRFLTLKPLPDSIIQESLEIQQGVNPFFIGRSEDCNCKIEDNRLSRVHCFIFKKRHAVGKSMYESPAQGLDDIWYCHTGTNVSYLNNNRMIQGTKFLLQDGDEIKIIWDKNNKFVIGFKVEINDTTGLFNEGLGMLQEQRVVLKQTAEEKDLVKKL 730
               SCOP domains d1j4la_ A: Phosphotyrosine binding domain of Rad53                                                                                                             SCOP domains
               CATH domains 1j4lA00 A:573-730  [code=2.60.200.20, no name defined]                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.........eee......eeee......ee..........eeeeeeee.............eeeeeeee.....eee..eee...eeee....eeee............eeeee....................ee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------FHA_DOMAIN  PDB: A:601-664 UniProt: 601-664                     ------------------------------------------------------------------ PROSITE
               Transcript 2 Exon 2.1  PDB: A:573-730 UniProt: 1-821 [INCOMPLETE]                                                                                                           Transcript 2
                 1j4l A 573 GNGRFLTLKPLPDSIIQESLEIQQGVNPFFIGRSEDCNCKIEDNRLSRVHCFIFKKRHAVGKSMYESPAQGLDDIWYCHTGTNVSYLNNNRMIQGTKFLLQDGDEIKIIWDKNNKFVIGFKVEINDTTGLFNEGLGMLQEQRVVLKQTAEEKDLVKKL 730
                                   582       592       602       612       622       632       642       652       662       672       682       692       702       712       722        

Chain P from PDB  Type:PROTEIN  Length:9
 aligned with RAD9_YEAST | P14737 from UniProtKB/Swiss-Prot  Length:1309

    Alignment length:9
           RAD9_YEAST   599 EVELTQELP 607
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
               Transcript 1 Exon 1.1  Transcript 1
                 1j4l P 599 EVELtQELP 607
                                |    
                              603-TPO

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J4L)

(-) Gene Ontology  (36, 42)

NMR Structure(hide GO term definitions)
Chain A   (RAD53_YEAST | P22216)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0004712    protein serine/threonine/tyrosine kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0000077    DNA damage checkpoint    A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006270    DNA replication initiation    The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0009202    deoxyribonucleoside triphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with triphosphate on the sugar.
    GO:0042326    negative regulation of phosphorylation    Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain P   (RAD9_YEAST | P14737)
molecular function
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0000077    DNA damage checkpoint    A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0044783    G1 DNA damage checkpoint    A cell cycle checkpoint that detects and negatively regulates progression from G1 to S phase in the cell cycle in response to DNA damage.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0031573    intra-S DNA damage checkpoint    A mitotic cell cycle checkpoint that slows DNA synthesis in response to DNA damage by the prevention of new origin firing and the stabilization of slow replication fork progression.
    GO:0031571    mitotic G1 DNA damage checkpoint    A mitotic cell cycle checkpoint that detects and negatively regulates progression through the G1/S transition of the cell cycle in response to DNA damage.
    GO:0008156    negative regulation of DNA replication    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
cellular component
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RAD53_YEAST | P222161dmz 1fhq 1fhr 1g3g 1g6g 1j4k 1j4o 1j4p 1j4q 1k2m 1k2n 1k3j 1k3n 1k3q 1qu5 2a0t 2jqi 2jql 2ygv 4pdp 4pds 5t2f 5t2s
        RAD9_YEAST | P147371fhr 1j4k 1j4p 1j4q 1k2m 1k2n 1k3n 1k3q 2ff4

(-) Related Entries Specified in the PDB File

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