PROSITE documentation PDOC00702

Cytidine and deoxycytidylate deaminases zinc-binding region signature and domain profile


Cytidine deaminase (EC (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (EC (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [1,2]. The deaminases possess either one or two conserved zinc-coordinating (Z) motifs, with the consensus amino acid signature H-x(1)-E-x(24,28)-P-C-x(2,4)-C. This motif is required for catalytic activity. Zinc coordination is mediated by a histidine and two cysteines [3]. The CMP/dCMP-type deaminase domain consists of a central β-sheet with one or more α helices on each side (see <PDB:1JTK>) [4].

Such a region is also found in other proteins [3,4,5,6]:

  • Yeast cytosine deaminase (EC (gene FCY1) which transforms cytosine into uracil.
  • Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA.
  • Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6- (ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6- (ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate.
  • Bacillus cereus blasticidin-S deaminase (EC, which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S.
  • Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA.
  • Bacillus subtilis tRNA-specific adenosine deaminase (tadA), catalyzes the deamination of adenosine to inosine at the wobble position of tRNAs.
  • Escherichia coli tRNA-specific adenosine deaminase (tadA), catalyzes the deamination of adenosine to inosine at the wobble position of tRNAs.
  • Yeast tRNA-specific adenosine deaminase subunit TAD2, deaminates adenosine- 34 to inosine in many tRNAs.

We have derived a signature pattern for this zinc-binding region. We also developed a profile which covers the entire CMP/dCMP-type deaminase domain.

Last update:

February 2015 / Text revised; profile added.

Technical section

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

CYT_DCMP_DEAMINASES_2, PS51747; Cytidine and deoxycytidylate deaminases domain profile  (MATRIX)

CYT_DCMP_DEAMINASES_1, PS00903; Cytidine and deoxycytidylate deaminases zinc-binding region signature  (PATTERN)


1AuthorsYang C., Carlow D., Wolfenden R., Short S.A.
TitleCloning and nucleotide sequence of the Escherichia coli cytidine deaminase (ccd) gene.
SourceBiochemistry 31:4168-4174(1992).
PubMed ID1567863

2AuthorsMoore J.T., Silversmith R.E., Maley G.F., Maley F.
TitleT4-phage deoxycytidylate deaminase is a metalloprotein containing two zinc atoms per subunit.
SourceJ. Biol. Chem. 268:2288-2291(1993).
PubMed ID8428902

3AuthorsShandilya S.M.D., Nalam M.N.L., Nalivaika E.A., Gross P.J., Valesano J.C., Shindo K., Li M., Munson M., Royer W.E., Harjes E., Kono T., Matsuo H., Harris R.S., Somasundaran M., Schiffer C.A.
TitleCrystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces.
SourceStructure 18:28-38(2010).
PubMed ID20152150

4AuthorsJohansson E., Mejlhede N., Neuhard J., Larsen S.
TitleCrystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution.
SourceBiochemistry 41:2563-2570(2002).
PubMed ID11851403

5AuthorsReizer J., Buskirk S., Bairoch A., Reizer A., Saier M.H. Jr.
TitleA novel zinc-binding motif found in two ubiquitous deaminase families.
SourceProtein Sci. 3:853-856(1994).
PubMed ID8061614

6AuthorsBhattacharya S., Navaratnam N., Morrison J.R., Scott J., Taylor W.R.
TitleCytosine nucleoside/nucleotide deaminases and apolipoprotein B mRNA editing.
SourceTrends Biochem. Sci. 19:105-106(1994).
PubMed ID8203015

PROSITE is copyright. It is produced by the SIB Swiss Institute Bioinformatics. There are no restrictions on its use by non-profit institutions as long as its content is in no way modified. Usage by and for commercial entities requires a license agreement. For information about the licensing scheme send an email to
Prosite License or see: prosite_license.html.


View entry in original PROSITE document format
View entry in raw text format (no links)