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(-) Description

Title :  SOLUTION STRUCTURE OF A ZINC DOMAIN CONSERVED IN YEAST COPPER-REGULATED TRANSCRIPTION FACTORS
 
Authors :  R. B. Turner, D. L. Smith, M. E. Zawrotny, M. F. Summers, M. C. Posewitz, D. R. Winge
Date :  04 Jun 99  (Deposition) - 10 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Metallothionein, Amt, Metal Regulation, Translation/Regulation Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. B. Turner, D. L. Smith, M. E. Zawrotny, M. F. Summers, M. C. Posewitz, D. R. Winge
Solution Structure Of A Zinc Domain Conserved In Yeast Copper-Regulated Transcription Factors.
Nat. Struct. Biol. V. 5 551 1998
PubMed-ID: 9665167  |  Reference-DOI: 10.1038/805
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (ACTIVATOR OF METALLOTHIONEIN 1)
    Chains: A
    Engineered: YES
    Fragment: RESIDUES 1-42
    Other Details: ZINC BINDING DOMAIN
    Other Details - Source: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN CANDIDA GLABRATA.
    Synonym: AMT1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (15x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:11 , CYS A:14 , CYS A:23 , HIS A:25BINDING SITE FOR RESIDUE ZN A 43
2ZNBAUTHORCYS A:11 , CYS A:14 , CYS A:23 , HIS A:25ZN METAL-BINDING SITE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CO4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CO4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CO4)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_FIST_1PS01119 Copper-fist DNA-binding domain signature.AMT1_CANGA1-39  1A:1-39
2COPPER_FIST_2PS50073 Copper-fist DNA-binding domain profile.AMT1_CANGA1-40  1A:1-40

(-) Exons   (0, 0)

(no "Exon" information available for 1CO4)

(-) 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:42
 aligned with AMT1_CANGA | P41772 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:42
                                    10        20        30        40  
            AMT1_CANGA    1 MVVINGVKYACDSCIKSHKAAQCEHNDRPLKILKPRGRPPTT 42
               SCOP domains d1co4a_ A:                                 SCOP domains
               CATH domains 1co4A00 A:1-42                             CATH domains
               Pfam domains ------------------------------------------ Pfam domains
         Sec.struct. author .eee..eeeeehhhh..hhhhh.......eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                PROSITE (1) COPPER_FIST_2  PDB: A:1-40 UniProt: 1-40-- PROSITE (1)
                PROSITE (2) COPPER_FIST_1  PDB: A:1-39             --- PROSITE (2)
                 Transcript ------------------------------------------ Transcript
                  1co4 A  1 MVVINGVKYACDSCIKSHKAAQCEHNDRPLKILKPRGRPPTT 42
                                    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: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CO4)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (AMT1_CANGA | P41772)
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:0001202    RNA polymerase II transcription factor activity, copper ion regulated core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a specific DNA sequence that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with copper(I) (Cu+) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+), such a way that copper ion binding regulates the activity of the transcription factor, perhaps by regulating the ability to interact 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), or by regulating some other function of the transcription factor, in order to modulate transcription by RNAP II.
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    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:0006878    cellular copper ion homeostasis    Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
    GO:0071280    cellular response to copper ion    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 a copper ion stimulus.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates 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:0046688    response to copper ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a copper ion stimulus.
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    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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