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154  structures 5079  species 3  interactions 17292  sequences 96  architectures

Family: dCMP_cyt_deam_1 (PF00383)

Summary: Cytidine and deoxycytidylate deaminase zinc-binding region

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Cytidine and deoxycytidylate deaminase zinc-binding region Provide feedback

No Pfam abstract.

Literature references

  1. 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

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.

Such a region is also found in other proteins [PUBMED:8061614, PUBMED:8203015]:

  • 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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan CDA (CL0109), which has the following description:

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 [2]. 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 16 members:

A_deamin AICARFT_IMPCHas APOBEC_C APOBEC_N Bd3614-deam dCMP_cyt_deam_1 dCMP_cyt_deam_2 DYW_deaminase LmjF365940-deam MafB19-deam OTT_1508_deam Pput2613-deam SCP1201-deam Toxin-deaminase XOO_2897-deam YwqJ-deaminase

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(59)
Full
(17292)
Representative proteomes NCBI
(12505)
Meta
(5590)
RP15
(1638)
RP35
(3063)
RP55
(4050)
RP75
(4759)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(59)
Full
(17292)
Representative proteomes NCBI
(12505)
Meta
(5590)
RP15
(1638)
RP35
(3063)
RP55
(4050)
RP75
(4759)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(59)
Full
(17292)
Representative proteomes NCBI
(12505)
Meta
(5590)
RP15
(1638)
RP35
(3063)
RP55
(4050)
RP75
(4759)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: dCMP_cyt_deam;
Type: Family
Author: Bateman A, Finn RD, Griffiths-Jones SR
Number in seed: 59
Number in full: 17292
Average length of the domain: 105.20 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 47.17 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 102
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

dCMP_cyt_deam_2 RibD_C dCMP_cyt_deam_1

Structures

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 154 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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