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(-) Description

Title :  GAL4 (CD), NMR, 24 STRUCTURES
 
Authors :  J. D. Baleja, G. Wagner
Date :  10 Oct 97  (Deposition) - 15 Apr 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (24x)
Keywords :  Transcription Regulation, Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Baleja, V. Thanabal, G. Wagner
Refined Solution Structure Of The Dna-Binding Domain Of Gal4 And Use Of 3J(113Cd, 1H) In Structure Determination.
J. Biomol. Nmr V. 10 397 1997
PubMed-ID: 9460244  |  Reference-DOI: 10.1023/A:1018332327565
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GAL4 (CD)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: XA-90
    Expression System Taxid: 562
    Fragment: DNA-BINDING DOMAIN
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  
NMR Structure (24x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 2)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION

(-) Sites  (4, 4)

NMR Structure (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:11 , CYS A:14 , CYS A:21 , CYS A:28 , CD A:45BINDING SITE FOR RESIDUE CD A 44
2AC2SOFTWARECYS A:11 , CYS A:28 , CYS A:31 , CYS A:38 , CD A:44BINDING SITE FOR RESIDUE CD A 45
3CD4UNKNOWNCYS A:11 , CYS A:14 , CYS A:21 , CYS A:28CADMIUM BINDING SITE.
4CD5UNKNOWNCYS A:11 , CYS A:28 , CYS A:31 , CYS A:38CADMIUM BINDING SITE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AW6)

(-) Cis Peptide Bonds  (1, 24)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24Lys A:25 -Pro A:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AW6)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZN2_CY6_FUNGAL_1PS00463 Zn(2)-C6 fungal-type DNA-binding domain signature.GAL4_YEAST10-38  1A:10-38
2ZN2_CY6_FUNGAL_2PS50048 Zn(2)-C6 fungal-type DNA-binding domain profile.GAL4_YEAST10-40  1A:10-40

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL248C1YPL248C.1XVI:82356-797112646GAL4_YEAST1-8818811A:1-4343

(-) 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:43
 aligned with GAL4_YEAST | P04386 from UniProtKB/Swiss-Prot  Length:881

    Alignment length:43
                                    10        20        30        40   
            GAL4_YEAST    1 MKLLSSIEQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPK 43
               SCOP domains d1aw6a_ A: Gal4                             SCOP domains
               CATH domains 1aw6A00 A:1-43 CD2-Gal4                     CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh...........hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------ZN2_CY6_FUNGAL_2  PDB: A:10-40 --- PROSITE (1)
                PROSITE (2) ---------ZN2_CY6_FUNGAL_1  PDB: A:10-3----- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:1-43 UniProt: 1-881        Transcript 1
                  1aw6 A  1 MKLLSSIEQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPK 43
                                    10        20        30        40
   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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AW6)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (GAL4_YEAST | P04386)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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:0001133    RNA polymerase II transcription factor activity, sequence-specific transcription regulatory region DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA by RNA polymerase II and recruiting another transcription factor to the DNA in order to modulate transcription by RNAP II.
    GO:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0001077    transcriptional activator 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 activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006012    galactose metabolic process    The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.
    GO:0000435    positive regulation of transcription from RNA polymerase II promoter by galactose    Any process involving galactose that activates or increases the rate 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: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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  1aw6
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  GAL4_YEAST | P04386
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 Related Entries

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

UniProtKB/Swiss-Prot
        GAL4_YEAST | P04386: 1d66 1hbw 3bts 3coq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AW6)