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(-) Description

Title :  SOLUTION STRUCTURE OF THE CDC13 DNA-BINDING DOMAIN COMPLEXED WITH A SINGLE-STRANDED TELOMERIC DNA 11-MER
 
Authors :  R. M. Mitton-Fry, E. M. Anderson, D. L. Theobald, L. W. Glustrom, D. S. Wuttke
Date :  14 Jan 04  (Deposition) - 04 May 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
Keywords :  Ssdna, Single-Stranded Nucleic Acid, Recognition, Specificity, Cdc13, Ob-Fold, Telomere, Nmr, Cell Cycle/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Mitton-Fry, E. M. Anderson, D. L. Theobald, L. W. Glustrom, D. S. Wuttke
Structural Basis For Telomeric Single-Stranded Dna Recognition By Yeast Cdc13
J. Mol. Biol. V. 338 241 2004
PubMed-ID: 15066429  |  Reference-DOI: 10.1016/J.JMB.2004.01.063
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELL DIVISION CONTROL PROTEIN 13
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DNA-BINDING DOMAIN
    Gene: CDC13, YDL220C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 2 - 5'-D(*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1S40)

(-) Sites  (0, 0)

(no "Site" information available for 1S40)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S40)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S40)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S40)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S40)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDL220C1YDL220C.1IV:65019-622452775CDC13_YEAST1-9249241A:5-191187

(-) 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:187
 aligned with CDC13_YEAST | P32797 from UniProtKB/Swiss-Prot  Length:924

    Alignment length:187
                                   509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       
          CDC13_YEAST   500 KMARKDPTIEFCQLGLDTFETKYITMFGMLVSCSFDKPAFISFVFSDFTKNDIVQNYLYDRYLIDYENKLELNEGFKAIMYKNQFETFDSKLRKIFNNGLRDLQNGRDENLSQYGIVCKMNIKVKMYNGKLNAIVRECEPVPHSQISSIASPSQCEHLRLFYQRAFKRIGESAISRYFEEYRRFFPI 686
               SCOP domains d1s40a_ A: CDC13 ssDNA-binding domain                                                                                                                                                       SCOP domains
               CATH domains 1s40A00 A:5-191 Nucleic acid-binding proteins                                                                                                                                               CATH domains
               Pfam domains ----------Telo_bind-1s40A01 A:15-191                                                                                                                                                        Pfam domains
         Sec.struct. author .........hhhhh.......eeeeeeeeeeeee.......eeeee............................eeee..hhhhhhhhhhhhhhhhh.hhhhhh............eeeeeeee.ee..ee..ee...ee....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-191 UniProt: 1-924 [INCOMPLETE]                                                                                                                                          Transcript 1
                 1s40 A   5 KMARKDPTIEFCQLGLDTFETKYITMFGMLVSCSFDKPAFISFVFSDFTKNDIVQNYLYDRYLIDYENKLELNEGFKAIMYKNQFETFDSKLRKIFNNGLRDLQNGRDENLSQYGIVCKMNIKVKMYNGKLNAIVRECEPVPHSQISSIASPSQCEHLRLFYQRAFKRIGESAISRYFEEYRRFFPI 191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       


Chain B from PDB  Type:DNA  Length:11
                                           
                 1s40 B   1 GTGTGGGTGTG  11
                                    10
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: OB (224)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (CDC13_YEAST | P32797)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0098505    G-rich strand telomeric DNA binding    Interacting selectively and non-covalently with G-rich, single-stranded, telomere-associated DNA.
    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:0043047    single-stranded telomeric DNA binding    Interacting selectively and non-covalently with single-stranded telomere-associated DNA.
    GO:0010521    telomerase inhibitor activity    Stops, prevents or reduces the activity of a telomerase. Telomerase catalyzes the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence.
biological process
    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:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0051974    negative regulation of telomerase activity    Any process that stops or reduces the activity of the enzyme telomerase, which catalyzes of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:0032210    regulation of telomere maintenance via telomerase    Any process that modulates the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0071166    ribonucleoprotein complex localization    Any process in which a ribonucleoprotein complex is transported to, or maintained in, a specific location within a cell.
    GO:0016233    telomere capping    A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
    GO:0000723    telomere maintenance    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
    GO:0007004    telomere maintenance via telomerase    The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase.
cellular component
    GO:1990879    CST complex    A complex formed by the association of Cdc13 (CTC1 in mammals) with Stn1 in yeast (OBFC1 in mammals) and Ten1 protein (also TEN1 in mammals) with single-stranded telomeric DNA. The CST complex plays a role in telomere protection.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CDC13_YEAST | P32797: 1kxl 3nws 3nwt 3oip 3oiq 4hce

(-) Related Entries Specified in the PDB File

1kxl SAME PROTEIN CONSTRUCT WITHOUT DNA MODELED