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(-) Description

Title :  STRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA
 
Authors :  B. Cahuzac, R. Cerdan, B. Felenbok, E. Guittet
Date :  14 Jun 00  (Deposition) - 28 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,P
Keywords :  Protein-Dna Complex, Zinc Binuclear Cluster Protein, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Cahuzac, R. Cerdan, B. Felenbok, E. Guittet
The Solution Structure Of An Alcr-Dna Complex Sheds Light Onto The Unique Tight And Monomeric Dna Binding Of A Zn(2)Cys(6) Protein.
Structure V. 9 827 2001
PubMed-ID: 11566132  |  Reference-DOI: 10.1016/S0969-2126(01)00640-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(P*CP*GP*TP*GP*CP*GP*GP*AP*TP*C)-3')
    Chains: A
    Engineered: YES
    Other Details: ALCR CONSENSUS HALF-TARGET
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(P*GP*AP*TP*CP*CP*GP*CP*AP*CP*G)-3')
    Chains: B
    Engineered: YES
    Other Details: ALCR CONSENSUS HALF-TARGET
    Synthetic: YES
 
Molecule 3 - ETHANOL REGULON TRANSCRIPTIONAL FACTOR
    Chains: P
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL DNA-BINDING DOMAIN, RESIDUES 1-60
    Mutation: YES
    Organism Scientific: EMERICELLA NIDULANS
    Organism Taxid: 162425
    Synonym: REGULATORY PROTEIN ALCR
    Variant: EMERICELLA

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS P:12 , CYS P:15 , CYS P:22 , CYS P:39 , ZN P:65BINDING SITE FOR RESIDUE ZN P 64
2AC2SOFTWARECYS P:12 , CYS P:39 , CYS P:42 , CYS P:49 , ZN P:64BINDING SITE FOR RESIDUE ZN P 65

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F5E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F5E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F5E)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZN2_CY6_FUNGAL_2PS50048 Zn(2)-C6 fungal-type DNA-binding domain profile.ALCR_EMENI11-51  1P:11-51

(-) Exons   (0, 0)

(no "Exon" information available for 1F5E)

(-) 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:DNA  Length:10
                                         
                  1f5e A  1 CGTGCGGATC 10
                                    10


Chain B from PDB  Type:DNA  Length:10
                                         
                  1f5e B  1 GATCCGCACG 10
                                    10


Chain P from PDB  Type:PROTEIN  Length:65
 aligned with ALCR_EMENI | P21228 from UniProtKB/Swiss-Prot  Length:821

    Alignment length:65
                              1                                                              
                              |      8        18        28        38        48        58     
            ALCR_EMENI    - --MADTRRRQNHSCDPCRKGKRRCDAPENRNEANENGWVSCSNCKRWNKDCTFNWLSSQRSKAKG 63
               SCOP domains d1f5ep_ P:                                                        SCOP domains
               CATH domains 1f5eP00 P:-1-63 CD2-Gal4                                          CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhh.......hhhhhhhh....hhhhhhh.....hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------ZN2_CY6_FUNGAL_2  PDB: P:11-51           ------------ PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  1f5e P -1 GSMADTRRRQNHSCDPCRKGKRRCDAPENRNEANENGWVSCSNCKRWNKDCTFNWLSSQRSKNSS 63
                                     8        18        28        38        48        58
   Legend:   → Mismatch (orange background)
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  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  (1, 1)

NMR Structure
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F5E)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain P   (ALCR_EMENI | P21228)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0046187    acetaldehyde catabolic process    The chemical reactions and pathways resulting in the breakdown of acetaldehyde, a colorless, flammable liquid intermediate in the metabolism of alcohol.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0006068    ethanol catabolic process    The chemical reactions and pathways resulting in the breakdown of ethanol, CH3-CH2-OH, a colorless, water-miscible, flammable liquid produced by alcoholic fermentation.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006567    threonine catabolic process    The chemical reactions and pathways resulting in the breakdown of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
    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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  1f5e
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALCR_EMENI | P21228: 1f4s 2alc 3alc

(-) Related Entries Specified in the PDB File

1f4s PROTEIN-DNA COMPLEX, 10 MODELS
2alc FREE PROTEIN, MINIMIZED AVERAGED STRUCTURE
3alc FREE PROTEIN, 17 MODELS