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
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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: | APOBEC1 APOBEC2 APOBEC3 APOBEC4_like APOBEC_N Bd3614-deam dCMP_cyt_deam_2 Inv-AAD Ldh_2 LmjF365940-deam MafB19-deam NAD1 NAD2 OTT_1508_deam SNAD4 XOO_2897-deam |
Similarity to PfamA using HHSearch: | LmjF365940-deam MafB19-deam Bd3614-deam SNAD4 APOBEC3 Inv-AAD |
External database links
PROSITE: | PDOC00702 |
SCOP: | 1ctt |
This tab holds annotation information from the InterPro database.
InterPro entry IPR002125
Cytidine deaminase (EC 3.5.4.5) (cytidine aminohydrolase) catalyses the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (EC 3.5.4.12) (dCMP deaminase) hydrolyses dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [PUBMED:1567863, PUBMED:8428902]. 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 [PUBMED:20152150]. The CMP/dCMP-type deaminase domain consists of a central beta-sheet with one or more alpha helices on each side [PUBMED:11851403].
This entry represents the CMP/dCMP-type deaminase domain. Some enzymes, such as riboflavin biosynthesis protein PYRR, have a non-functional deaminase domain that lacks the catalytically essential zinc-binding residues [PUBMED:23150645].
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 33 members:
A_deamin AICARFT_IMPCHas AID APOBEC1 APOBEC2 APOBEC3 APOBEC4 APOBEC4_like APOBEC_C APOBEC_N Bd3614-deam DAAD dCMP_cyt_deam_1 dCMP_cyt_deam_2 DYW_deaminase FdhD-NarQ Inv-AAD LmjF365940-deam LpxI_C MafB19-deam NAD1 NAD2 OTT_1508_deam Pput2613-deam SCP1201-deam SNAD1 SNAD2 SNAD3 SNAD4 TM1506 Toxin-deaminase XOO_2897-deam YwqJ-deaminaseAlignments
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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 (46) |
Full (26475) |
Representative proteomes | UniProt (66416) |
NCBI (114683) |
Meta (5570) |
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RP15 (6884) |
RP35 (17228) |
RP55 (25767) |
RP75 (35627) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (46) |
Full (26475) |
Representative proteomes | UniProt (66416) |
NCBI (114683) |
Meta (5570) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (6884) |
RP35 (17228) |
RP55 (25767) |
RP75 (35627) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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
Seed source: | Prosite |
Previous IDs: | dCMP_cyt_deam; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 46 |
Number in full: | 26475 |
Average length of the domain: | 107.50 aa |
Average identity of full alignment: | 24 % |
Average coverage of the sequence by the domain: | 45.40 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 101 | ||||||||||||
Family (HMM) version: | 23 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 6 interactions for this family. More...
dCMP_cyt_deam_1 THUMP dCMP_cyt_deam_2 RibD_C RibD_C dCMP_cyt_deam_2Structures
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 212 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 sequence.
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