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(-) Description

Title :  THE DNA BINDING DOMAIN OF RTBP1
 
Authors :  W. Lee, S. Ko
Date :  22 Mar 08  (Deposition) - 24 Mar 09  (Release) - 24 Mar 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Telomere Binding Protein, Plant, Nucleus, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ko, E. Y. Yu, J. Shin, H. H. Yoo, T. Tanaka, W. T. Kim, H. S. Cho, W. Lee, I. K. Chung
Solution Structure Of The Dna Binding Domain Of Rice Telomere Binding Protein Rtbp1
Biochemistry V. 48 827 2009
PubMed-ID: 19152316  |  Reference-DOI: 10.1021/BI801270G
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TELOMERE BINDING PROTEIN-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector: PGEX 4T-1
    Expression System Vector Type: VECTOR
    Fragment: DNA BINDING DOMAIN
    Organism Common: RICE
    Organism Scientific: ORYZA SATIVA
    Organism Taxid: 4530
    Synonym: RTBP1

 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 2ROH)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_MYBPS51294 Myb-type HTH DNA-binding domain profile.TBP1_ORYSJ529-588  1A:26-85

(-) Exons   (0, 0)

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(-) 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    
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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:122
 aligned with TBP1_ORYSJ | Q9LL45 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:150
                                   493       503       513       523       533       543       553       563       573       583       593       603       613       623       633
           TBP1_ORYSJ   484 GSVDYPVEWSTQETSASSQAIVPFADPNSLALANVPLSRSKRPDFGQRRIRRPFTVAEVELLVEAVEHLGTGRWRDVKFRAFENVHHRTYVDLKDKWKTLVHTASIAPQQRRGAPVPQELLDRVLAAQAYWSEQQAKLHGDPPVPEICPT 633
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..--------------------................................hhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh...---.-----..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------HTH_MYB  PDB: A:26-85 UniProt: 529-588                      --------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2roh A   1 GS--------------------PFADPNSLALANVPLSRSKRPDFGQRRIRRPFTVAEVELLVEAVEHLGTGRWRDVKFRAFENVHHRTYVDLKDKWKTLVHTASIAPQQRRGAPVPQELLDRVLAAQAYWSVDSS---G-----RIVTL 122
                             |       -         -  |     10        20        30        40        50        60        70        80        90       100       110     | 117     | 122
                             2                    3                                                                                                              116 117   118
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ROH)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (TBP1_ORYSJ | Q9LL45)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003691    double-stranded telomeric DNA binding    Interacting selectively and non-covalently with double-stranded telomere-associated DNA.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0042162    telomeric DNA binding    Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
biological process
    GO:0032204    regulation of telomere maintenance    Any process that modulates the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
    GO:0031627    telomeric loop formation    The process in which linear telomeric DNA is remodeled into duplex loops, by the invasion of a 3' single-stranded overhang into the duplex region.
cellular component
    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:0000783    nuclear telomere cap complex    A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome.

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