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(-) Description

Title :  STRUCTURES OF DNA-BINDING MUTANT ZINC FINGER DOMAINS: IMPLICATIONS FOR DNA BINDING
 
Authors :  R. C. Hoffman, R. X. Xu, S. J. Horvath, J. R. Herriott, R. E. Klevit
Date :  01 Oct 93  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. C. Hoffman, S. J. Horvath, R. E. Klevit
Structures Of Dna-Binding Mutant Zinc Finger Domains: Implications For Dna Binding.
Protein Sci. V. 2 951 1993
PubMed-ID: 8318900
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YEAST TRANSCRIPTION FACTOR ADR1
    Chains: A
    Engineered: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:106 , VAL A:108 , CYS A:109 , HIS A:122 , HIS A:126BINDING SITE FOR RESIDUE ZN A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ADR1_YEAST106-126
134-155		  1A:106-126
-

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR216W1YDR216W.1IV:895032-8990033972ADR1_YEAST1-132313231A:102-13029

(-) 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:29
 aligned with ADR1_YEAST | P07248 from UniProtKB/Swiss-Prot  Length:1323

    Alignment length:29
                                   111       121         
           ADR1_YEAST   102 RSFVCEVCTRAFARQEHLKRHYRSHTNEK 130
               SCOP domains d1arfa_ A: ADR1               SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author ..eee...eeee..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----ZINC_FINGER_C2H2_1   ---- PROSITE
               Transcript 1 Exon 1.1  PDB: A:102-130      Transcript 1
                 1arf A 102 RSFVCEVCTRAFARQEYLKRHYRSHTNEK 130
                                   111       121
   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: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ARF)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (ADR1_YEAST | P07248)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0001093    TFIIB-class transcription factor binding    Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIB class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
    GO:0001094    TFIID-class transcription factor binding    Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000982    transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    GO:0001190    transcriptional activator activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
    GO:0071400    cellular response to oleic acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oleic acid stimulus.
    GO:0006325    chromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
    GO:0031936    negative regulation of chromatin silencing    Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing.
    GO:0007031    peroxisome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.
    GO:0061425    positive regulation of ethanol catabolic process by 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 and activates or increases the frequency, rate or extent of an ethanol catabolic process.
    GO:0097235    positive regulation of fatty acid beta-oxidation by positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of fatty acid beta-oxidation by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0061424    positive regulation of peroxisome organization by 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 and activates or increases the frequency, rate or extent of peroxisome organization.
    GO:0061429    positive regulation of transcription from RNA polymerase II promoter by oleic acid    Any process involving oleic acid that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0061410    positive regulation of transcription from RNA polymerase II promoter in response to ethanol    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an ethanol stimulus.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        ADR1_YEAST | P07248: 1ard 1are 1paa 2adr 5a7u

(-) Related Entries Specified in the PDB File

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