PROSITE documentation PDOC00378
Zn(2)-C6 fungal-type DNA-binding domain signature and profile


A number of fungal transcriptional activator proteins contain a cysteine-rich region that binds DNA in a zinc-dependent fashion. It has been shown [1,2] that this region forms a binuclear zinc cluster where six conserved cysteines bind two zinc cations. Some proteins known to contain such a domain are listed below [3].

  Gene name(s)      Biological source        Scope of activatory action
  ---------------   ---------------------    ---------------------------------
  aflR              Aspergillus              Aflatoxin biosynthesis
  amdR or intA      Emericella nidulans      Amides catabolism
  ARGR2 or ARG81    Yeast                    Arginine metabolism
  CAT8 or MSP8      Yeast                    Gluconeogenic enzymes
  CBF3B or CEP3     Yeast                    Chromosome segregation
  CHA4              Yeast                    L-serine dehydratase
  CYP1 or HAP1      Yeast                    Iso-1 and iso-2 cytochrome c
  CZF1              Candida albicans         Unknown
  GAL4              Yeast                    Galactose metabolism
  LAC9              Kluyveromyces lactis     Galactose metabolism
  LEU3              Yeast                    Leucine biosynthesis
  LYS14             Yeast                    Lysine biosynthesis
  MAL1R or MAL13    Yeast                    Maltose metabolism
  MAL3R or MAL33    Yeast                    Maltose metabolism
  MAL6R or MAL63    Yeast                    Maltose metabolism
  nirA              Emericella nidulans      Nitrate assimilation
  nit-4             Neurospora crassa        Nitrate assimilation
  PDR1 or CYH3      Yeast                    Permeability
  PDR3              Yeast                    Permeability ?
  PIP2              Yeast                    Peroxisome proliferation
  PPR1              Yeast                    Pyrimidine metabolism
  PUT3              Yeast                    Proline metabolism
  qa-1f             Neurospora crassa        Quinate metabolism
  qutA              Emericella nidulans      Quinate metabolism
  SEF1              Yeast & K.lactis         ?
  SIP4              Yeast                    Unknown
  STB5              Yeast                    Unknown
  SUC1              Candida albicans         Sucrose utilization
  TEA1              Yeast                    Ty1 enhancer binding
  thi1 or ntf1      Fission yeast            Thiamine repressible genes
  THI2              Yeast                    Thiamine biosynthesis
  uaY               Emericella nidulans      Purine utilization
  UGA3              Yeast                    GABA catabolism
  UGA35 or DAL81    Yeast                    GABA, urea, arginine, allantoin
                                             and catabolism
  UME6              Yeast                    Many genes such as arginase,
                                             sporulation genes, etc.

  YAL051w           Yeast                    ? (Chromosome I)
  YBR033w           Yeast                    ? (Chromosome II)
  YBR150c           Yeast                    ? (Chromosome II)
  YBR239c           Yeast                    ? (Chromosome II)
  YCR106w           Yeast                    ? (Chromosome III)
  YDR213c           Yeast                    ? (Chromosome IV)
  YDR303c           Yeast                    ? (Chromosome IV)
  YDR421w           Yeast                    ? (Chromosome IV)
  YDR520c           Yeast                    ? (Chromosome IV)
  YER184c           Yeast                    ? (Chromosome V)
  YFL052w           Yeast                    ? (Chromosome VI)
  YHR056c           Yeast                    ? (Chromosome VIII)
  YIL130w           Yeast                    ? (Chromosome IX)
  YJL103c           Yeast                    ? (Chromosome X)
  YJL206c           Yeast                    ? (Chromosome X)
  YKL038w           Yeast                    ? (Chromosome XI)
  YKL222c           Yeast                    ? (Chromosome XI)
  YKR064w           Yeast                    ? (Chromosome XI)
  YLR278c           Yeast                    ? (Chromosome XII)
  YML076c           Yeast                    ? (Chromosome XIII)
  YMR019w           Yeast                    ? (Chromosome XIII)
  YNR063w           Yeast                    ? (Chromosome XIV)
  YPL133c           Yeast                    ? (Chromosome XVI)

The spacing of the cysteines in this type of domain is C-x(2)-C-x(6)-C-x(5 to 12)-C-x(2)-C-x(6 to 8)-C. There are also a number of other conserved residues in the loop regions between the cysteines which can be used to help define a specific pattern for such a domain. This domains is generally found in the N-terminal section of these proteins with the exception of UME6 where it is found in the C-terminal section.

Last update:

March 2005 / Text revised.


Technical section

PROSITE methods (with tools and information) covered by this documentation:

ZN2_CY6_FUNGAL_2, PS50048; Zn(2)-C6 fungal-type DNA-binding domain profile  (MATRIX)

ZN2_CY6_FUNGAL_1, PS00463; Zn(2)-C6 fungal-type DNA-binding domain signature  (PATTERN)


1AuthorsPan T. Coleman J.E.
TitleGAL4 transcription factor is not a 'zinc finger' but forms a Zn(II)2Cys6 binuclear cluster.
SourceProc. Natl. Acad. Sci. U.S.A. 87:2077-2081(1990).
PubMed ID2107541

2AuthorsMarmorstein R. Carey M. Ptashne M. Harrison S.C.
TitleDNA recognition by GAL4: structure of a protein-DNA complex.
SourceNature 356:408-414(1992).
PubMed ID1557122

3AuthorsSchjerling P. Holmberg S.
TitleComparative amino acid sequence analysis of the C6 zinc cluster family of transcriptional regulators.
SourceNucleic Acids Res. 24:4599-4607(1996).
PubMed ID8967907

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