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{PDOC00702}
{PS00903; CYT_DCMP_DEAMINASES_1}
{PS51747; CYT_DCMP_DEAMINASES_2}
{BEGIN}
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* Cytidine and deoxycytidylate deaminases zinc-binding region signature and domain profile *
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Cytidine deaminase   (EC  3.5.4.5)  (cytidine  aminohydrolase)  catalyzes  the
hydrolysis of   cytidine   into  uridine  and  ammonia  while  deoxycytidylate
deaminase  (EC 3.5.4.12)  (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 beta-sheet with one or more alpha 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 3.5.4.1) (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 3.5.4.23),  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.

-Consensus pattern: [CH]-[AGV]-E-x(2)-[LIVMFGAT]-[LIVM]-x(17,33)-P-C-x(2,8)-C-
                    x(3)-[LIVM]
                    [The C's and H are zinc ligands]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: 1.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Last update: February 2015 / Text revised; profile added.

[ 1] Yang C., Carlow D., Wolfenden R., Short S.A.
     "Cloning and nucleotide sequence of the Escherichia coli cytidine
     deaminase (ccd) gene."
     Biochemistry 31:4168-4174(1992).
     PubMed=1567863
[ 2] Moore J.T., Silversmith R.E., Maley G.F., Maley F.
     "T4-phage deoxycytidylate deaminase is a metalloprotein containing two
     zinc atoms per subunit."
     J. Biol. Chem. 268:2288-2291(1993).
     PubMed=8428902
[ 3] Shandilya 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.
     "Crystal structure of the APOBEC3G catalytic domain reveals potential
     oligomerization interfaces."
     Structure 18:28-38(2010).
     PubMed=20152150; DOI=10.1016/j.str.2009.10.016
[ 4] Johansson E., Mejlhede N., Neuhard J., Larsen S.
     "Crystal structure of the tetrameric cytidine deaminase from Bacillus
     subtilis at  2.0 A resolution."
     Biochemistry 41:2563-2570(2002).
     PubMed=11851403
[ 5] Reizer J., Buskirk S., Bairoch A., Reizer A., Saier M.H. Jr.
     "A novel zinc-binding motif found in two ubiquitous deaminase
     families."
     Protein Sci. 3:853-856(1994).
     PubMed=8061614
[ 6] Bhattacharya S., Navaratnam N., Morrison J.R., Scott J., Taylor W.R.
     "Cytosine nucleoside/nucleotide deaminases and apolipoprotein B mRNA
     editing."
     Trends Biochem. Sci. 19:105-106(1994).
     PubMed=8203015

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