Summary: Cytidine and deoxycytidylate deaminase zinc-binding region
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Cytidine and deoxycytidylate deaminase zinc-binding region Provide feedback
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Bhattacharya S, Navaratnam N, Morrison JR, Scott J, Taylor WR; , Trends Biochem Sci 1994;19:105-106.: Cytosine nucleoside/nucleotide deaminases and apolipoprotein B mRNA editing. PUBMED:8203015 EPMC:8203015
Internal database links
|SCOOP:||PhnH APOBEC_N dCMP_cyt_deam_2 DUF2685 LmjF365940-deam Pput2613-deam MafB19-deam Bd3614-deam XOO_2897-deam|
|Similarity to PfamA using HHSearch:||LmjF365940-deam MafB19-deam Bd3614-deam|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002125
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 [PUBMED:1567863, PUBMED:8428902]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion.
- 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.
- B. subtilis hypothetical protein yaaJ.
- Escherichia coli hypothetical protein yfhC.
- Yeast hypothetical protein YJL035c.
|Molecular function||hydrolase activity (GO:0016787)|
|zinc ion binding (GO:0008270)|
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This clan contains both free nucleotide and nucleic acid deaminases that act on adenosine, cytosine, guanine and cytidine, and are collectively known as the deaminase superfamily. The conserved fold consists of a three-layered alpha/beta/alpha structure with 3 helices and 4 strands in the 2134 order [1,2].This superfamily is further divided into two major divisions based on the presence of a helix (helix-4) that renders the terminal strands (strands 4 and 5) either parallel to each other in its presence, or anti-parallel in its absence . Structurally, the deaminase-like fold is present in four other superfamilies including the JAB-like metalloproteins, the C-terminal AICAR transformylase-catalyzing domains of PurH, Tm1506 and the formate dehydrogenase accessory subunit FdhD. The active site of the deaminases is composed of three residues that coordinate a zinc ion between conserved helices 2 and 3. The residues are typically found as [HCD]xE and CxxC motifs at the beginning of helices 2 and 3. The zinc ion activates a water molecule, which forms a tetrahderal intermediate with the carbon atom that is linked to the amine group. This is followed by deamination of the base.
The clan contains the following 17 members:A_deamin AICARFT_IMPCHas APOBEC_C APOBEC_N Bd3614-deam dCMP_cyt_deam_1 dCMP_cyt_deam_2 DYW_deaminase FdhD-NarQ LmjF365940-deam MafB19-deam OTT_1508_deam Pput2613-deam SCP1201-deam Toxin-deaminase XOO_2897-deam YwqJ-deaminase
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Curation and family details
|Author:||Bateman A, Finn RD, Griffiths-Jones SR|
|Number in seed:||46|
|Number in full:||72107|
|Average length of the domain:||102.80 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||47.59 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the dCMP_cyt_deam_1 domain has been found. There are 199 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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