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(-) Description

Title :  SOLUTION STRUCTURE OF ARID DOMAIN OF ADR6 FROM SACCHAROMYCES CEREVISIAE
 
Authors :  X. Tu, J. Wu, Y. Xu, Y. Shi
Date :  18 Dec 01  (Deposition) - 17 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Adr6, Arid Domain, Dna-Binding, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Tu, J. Wu, Y. Xu, Y. Shi
1H, 13C And 15N Resonance Assignments And Secondary Structure Of Adr6 Dna-Binding Domain.
J. Biomol. Nmr V. 21 187 2001
PubMed-ID: 11727987  |  Reference-DOI: 10.1023/A:1012434510376
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION REGULATORY PROTEIN ADR6
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PREP-4
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: ARID DOMAIN
    Gene: ADR6
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: TRANSCRIPTION REGULATORY PROTEIN SWI1

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1KN5)

(-) Sites  (0, 0)

(no "Site" information available for 1KN5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KN5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KN5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KN5)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARIDPS51011 ARID domain profile.SWI1_YEAST406-493  1A:4-91

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL016W1YPL016W.1XVI:521011-5249553945SWI1_YEAST1-131413141A:3-104102

(-) 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:102
 aligned with SWI1_YEAST | P09547 from UniProtKB/Swiss-Prot  Length:1314

    Alignment length:102
                                   414       424       434       444       454       464       474       484       494       504  
           SWI1_YEAST   405 NNKQYELFMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQISDYQQLESIYFRILLPYERHMISQEGIKETQAKRI 506
               SCOP domains d1kn5a_ A: Transcription regulator Adr6 (Swi1)                                                         SCOP domains
               CATH domains 1kn5A00 A:3-104  [code=1.10.150.60, no name defined]                                                   CATH domains
               Pfam domains ARID-1kn5A01 A:3-87                                                                  ----------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...............hhhhhhhhhh...hhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -ARID  PDB: A:4-91 UniProt: 406-493                                                      ------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-104 UniProt: 1-1314 [INCOMPLETE]                                                    Transcript 1
                 1kn5 A   3 NNKQYELFMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQISDYQQLESIYFRILLPYERHMISQEGIKETQAKRI 104
                                    12        22        32        42        52        62        72        82        92       102
   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 alpha proteins (14657)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: ARID] (8)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (SWI1_YEAST | P09547)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0015616    DNA translocase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule.
    GO:0001102    RNA polymerase II activating transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0043044    ATP-dependent chromatin remodeling    Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
    GO:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
    GO:0000436    carbon catabolite activation of transcription from RNA polymerase II promoter    Any process involving carbon catabolites that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0044109    cellular alcohol catabolic process    The chemical reactions and pathways resulting in the breakdown of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom, occurring at the level of the individual cell.
    GO:0031496    positive regulation of mating type switching    Any process that activates or increases the frequency, rate or extent of mating type switching.
    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:0061412    positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation    Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of amino acids.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0005987    sucrose catabolic process    The chemical reactions and pathways resulting in the breakdown of sucrose, the disaccharide fructofuranosyl-glucopyranoside.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016514    SWI/SNF complex    A SWI/SNF-type complex that contains nine or more proteins, including both conserved (core) and nonconserved components; the Swi2/Snf2 ATPase is one of the core components.
    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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  1kn5
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  SWI1_YEAST | P09547
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 Related Entries

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

UniProtKB/Swiss-Prot
        SWI1_YEAST | P09547: 1kkx 2li6

(-) Related Entries Specified in the PDB File

5061 5061 IS CHEMICAL_SHIFTS FOR THIS PROTEIN.
1kkx 1KKX IS THE ENSEMBLE OF 10 STRUCTURES.