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(-) Description

Title :  THE SAP DOMAIN IS A DNA-BINDING DOMAIN CAPABLE OF BINDING S/MAR DNA
 
Authors :  J. O. B. Jacobsen, S. M. V. Freund, M. Bycroft
Date :  16 Jul 02  (Deposition) - 08 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  S  (20x)
Keywords :  Sap Domain, Dna Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. O. B. Jacobsen, S. M. V. Freund, M. Bycroft
The Sap Domain Is A Dna-Binding Domain Capable Of Binding S/Mar Dna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THO1 PROTEIN
    Chains: S
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGRO
    Expression System Strain: C41
    Expression System Taxid: 562
    Fragment: SAP DOMAIN, RESIDUES 2-50
    Organism Common: BAKERS YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1H1J)

(-) Sites  (0, 0)

(no "Site" information available for 1H1J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H1J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H1J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H1J)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAPPS50800 SAP motif profile.THO1_YEAST4-38  1S:5-39

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YER063W1YER063W.1V:281708-282364657THO1_YEAST1-2182181S:2-4443

(-) 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 S from PDB  Type:PROTEIN  Length:44
 aligned with THO1_YEAST | P40040 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:44
                             1                                          
                             |       9        19        29        39    
            THO1_YEAST    - -MADYSSLTVVQLKDLLTKRNLSVGGLKNELVQRLIKDDEESKG 43
               SCOP domains d1h1js_ S: S/mar DNA-binding protein Tho1    SCOP domains
               CATH domains 1h1jS00 S:1-44                               CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE ----SAP  PDB: S:5-39 UniProt: 4-38     ----- PROSITE
               Transcript 1 -Exon 1.1  PDB: S:2-44 UniProt: 1-218        Transcript 1
                  1h1j S  1 GSADYSSLTVVQLKDLLTKRNLSVGGLKNELVQRLIKDDEESKG 44
                                    10        20        30        40
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H1J)

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain S   (THO1_YEAST | P40040)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
biological process
    GO:0016973    poly(A)+ mRNA export from nucleus    The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
    GO:0022618    ribonucleoprotein complex assembly    The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        THO1_YEAST | P40040: 2wqg 4uzw 4uzx

(-) Related Entries Specified in the PDB File

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