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(-) Description

Title :  SOLUTION STRUCTURE OF A CCHHC DOMAIN OF NEURAL ZINC FINGER FACTOR-1
 
Authors :  H. J. Berkovits-Cymet, B. T. Amann, J. M. Berg
Date :  03 Jul 03  (Deposition) - 10 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (21x)
Keywords :  Cchhc Zinc Binding Domain, Neural Zinc Finger Factor-1, Dna Binding Domain, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Berkovits-Cymet, B. T. Amann, J. M. Berg
Solution Structure Of A Cchhc Domain Of Neural Zinc Finger Factor-1 And Its Implications For Dna Binding.
Biochemistry V. 43 898 2004
PubMed-ID: 14744132
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEURAL ZINC FINGER TRANSCRIPTION FACTOR 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNZF-1E
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ZINC BINDING DOMAIN, CCHHC DOMAIN
    Gene: NZF-1
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  
NMR Structure (21x): 

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:20 , CYS A:25 , HIS A:38 , CYS A:44 , GLU A:53BINDING SITE FOR RESIDUE ZN A 64

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_CCHHCPS51802 Zinc finger CCHHC-type profile.MYT1L_RAT22-65
496-539
540-583
895-938
944-987
997-1040		  1-
-
A:55-63
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1PXE)

(-) 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:48
 aligned with MYT1L_RAT | P70475 from UniProtKB/Swiss-Prot  Length:1187

    Alignment length:48
                                   510       520       530       540        
            MYT1L_RAT   501 RESKCPTPGCDGTGHVTGLYPHHRSLSGCPHKDRVPPEILAMHENVLK 548
               SCOP domains d1pxea_ A:                                       SCOP domains
               CATH domains ------------------------------------------------ CATH domains
           Pfam domains (1) ---------------------------------------------zf- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------zf- Pfam domains (2)
         Sec.struct. author ................................................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ZF_CCHHC  PDB: - UniProt: 496-539      ZF_CCHHC  PROSITE
                 Transcript ------------------------------------------------ Transcript
                 1pxe A  16 RESKCPTPGCDGTGHVTGLYPHHRSLSGCPHKDRVPPEILAMHENVLK  63
                                    25        35        45        55
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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  (0, 0)

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

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: no clan defined [family: zf-C2HC] (3)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (MYT1L_RAT | P70475)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001105    RNA polymerase II transcription coactivator activity    Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0044323    retinoic acid-responsive element binding    Interacting selectively and non-covalently with a retinoic acid-responsive element, a variable direct repeat of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    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: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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