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(-) Description

Title :  SOLUTION STRUCTURE OF RTT103 CTD INTERACTING DOMAIN
 
Authors :  B. M. Lunde, S. Reichow, M. Kim, T. C. Leeper, R. Becker, S. Buratowski, A. Meinhart, G. Varani
Date :  20 Jul 09  (Deposition) - 08 Sep 10  (Release) - 20 Oct 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Ctd-Interacting Domain, Rna Polymerase Ii Binding Protein, Phosphoprotein, Transcription Termination, Dna-Binding, Nucleus, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. M. Lunde, S. L. Reichow, M. Kim, H. Suh, T. C. Leeper, F. Yang, H. Mutschler, S. Buratowski, A. Meinhart, G. Varani
Cooperative Interaction Of Transcription Termination Factor With The Rna Polymerase Ii C-Terminal Domain.
Nat. Struct. Mol. Biol. V. 17 1195 2010
PubMed-ID: 20818393  |  Reference-DOI: 10.1038/NSMB.1893

(-) Compounds

Molecule 1 - REGULATOR OF TY1 TRANSPOSITION PROTEIN 103
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL-21(DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-131
    Gene: RTT103, YDR289C
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KM4)

(-) Sites  (0, 0)

(no "Site" information available for 2KM4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KM4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KM4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KM4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2KM4)

(-) Exons   (0, 0)

(no "Exon" information available for 2KM4)

(-) 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:137
 aligned with RT103_YEAST | Q05543 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
          RT103_YEAST     2 PFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIFSKQVVNDIERSLKTESSPVEALVLPQKLKDFAKDYEKLVKMHH 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------CTD_bind-2km4A01 A:57-120                                       ------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh------------------------hhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2km4 A   2 AFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIFSKQVVNDIERSLAA------------------------ALEHH 138
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 |       -         -      |137 
                                                                                                                                                             133                      134
   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  (0, 0)

(no "SCOP Domain" information available for 2KM4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KM4)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: CTD_bind] (2)

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (RT103_YEAST | Q05543)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000993    RNA polymerase II core binding    Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.
biological process
    GO:0042769    DNA damage response, detection of DNA damage    The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal.
    GO:0031124    mRNA 3'-end processing    Any process involved in forming the mature 3' end of an mRNA molecule.
    GO:0010526    negative regulation of transposition, RNA-mediated    Any process that decreases the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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.
    GO:0035861    site of double-strand break    A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix.

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  RT103_YEAST | Q05543
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 Related Entries

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

UniProtKB/Swiss-Prot
        RT103_YEAST | Q05543: 2l0i 5lvf

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