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226  structures 8904  species 0  interactions 30094  sequences 256  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 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-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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

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
(30094)
Representative proteomes UniProt
(114597)
RP15
(4683)
RP35
(14495)
RP55
(28909)
RP75
(47005)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(46)
Full
(30094)
Representative proteomes UniProt
(114597)
RP15
(4683)
RP35
(14495)
RP55
(28909)
RP75
(47005)
Alignment:
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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
(46)
Full
(30094)
Representative proteomes UniProt
(114597)
RP15
(4683)
RP35
(14495)
RP55
(28909)
RP75
(47005)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Finn RD , Griffiths-Jones SR
Number in seed: 46
Number in full: 30094
Average length of the domain: 107.70 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 45.04 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 101
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

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Selections

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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 226 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0P0WYM0 View 3D Structure Click here
A0A0R0FBZ7 View 3D Structure Click here
A0A0R0GCM7 View 3D Structure Click here
A0A0R0IBM9 View 3D Structure Click here
A0A0R0J2N5 View 3D Structure Click here
A0A0R0KFE2 View 3D Structure Click here
A0A0R4J4W5 View 3D Structure Click here
A0A1D6EFG6 View 3D Structure Click here
A0A1D6ELV0 View 3D Structure Click here
A0A1D6G380 View 3D Structure Click here
A0A1D6GAU5 View 3D Structure Click here
A0A1D6HWL4 View 3D Structure Click here
A0A1D6J3S7 View 3D Structure Click here
A0A1D6JLB3 View 3D Structure Click here
A0A1D6L0Y1 View 3D Structure Click here
A0A1D6NE76 View 3D Structure Click here
A0A1D8PE88 View 3D Structure Click here
A0A1D8PFW6 View 3D Structure Click here
A0A1D8PGE9 View 3D Structure Click here
A0A1D8PMQ1 View 3D Structure Click here
A0A2R8RZC9 View 3D Structure Click here
A1YLY2 View 3D Structure Click here
A1YLY4 View 3D Structure Click here
A4HUI5 View 3D Structure Click here
A4HXA3 View 3D Structure Click here
A4I830 View 3D Structure Click here
B4FPE0 View 3D Structure Click here
B6TRH4 View 3D Structure Click here
B7E8M5 View 3D Structure Click here
C6SVU5 View 3D Structure Click here
D4AC20 View 3D Structure Click here
F1QSJ0 View 3D Structure Click here
F4KH86 View 3D Structure Click here
I1JK94 View 3D Structure Click here
I1K0B7 View 3D Structure Click here
I1K641 View 3D Structure Click here
I1KPS1 View 3D Structure Click here
I1L699 View 3D Structure Click here
I1LYE2 View 3D Structure Click here
I1M485 View 3D Structure Click here
I1MS02 View 3D Structure Click here
I1N3Z5 View 3D Structure Click here
K7KK60 View 3D Structure Click here
K7L068 View 3D Structure Click here
K7MK44 View 3D Structure Click here
K7N544 View 3D Structure Click here
M0RA73 View 3D Structure Click here
O05791 View 3D Structure Click here
O43012 View 3D Structure Click here
O53839 View 3D Structure Click here
O59834 View 3D Structure Click here
O65571 View 3D Structure Click here
O65896 View 3D Structure Click here
O69719 View 3D Structure Click here
O94642 View 3D Structure Click here
P06773 View 3D Structure Click here
P0ABF6 View 3D Structure Click here
P25539 View 3D Structure Click here
P30648 View 3D Structure Click here
P32320 View 3D Structure Click here
P32321 View 3D Structure Click here
P34401 View 3D Structure Click here
P47058 View 3D Structure Click here
P56389 View 3D Structure Click here
P68398 View 3D Structure Click here
P78594 View 3D Structure Click here
P87241 View 3D Structure Click here
P9WPH1 View 3D Structure Click here
P9WPH3 View 3D Structure Click here
Q06549 View 3D Structure Click here
Q09190 View 3D Structure Click here
Q0D7H8 View 3D Structure Click here
Q10M63 View 3D Structure Click here
Q10SM6 View 3D Structure Click here
Q12178 View 3D Structure Click here
Q12362 View 3D Structure Click here
Q1PEH3 View 3D Structure Click here
Q20628 View 3D Structure Click here
Q22922 View 3D Structure Click here
Q2FXF9 View 3D Structure Click here
Q2FY04 View 3D Structure Click here
Q2G2A1 View 3D Structure Click here
Q4D469 View 3D Structure Click here
Q4DCG1 View 3D Structure Click here
Q54DP5 View 3D Structure Click here
Q54DQ7 View 3D Structure Click here
Q54I82 View 3D Structure Click here
Q54JE5 View 3D Structure Click here
Q54M63 View 3D Structure Click here
Q54SS3 View 3D Structure Click here
Q54SW5 View 3D Structure Click here
Q559S7 View 3D Structure Click here
Q561R2 View 3D Structure Click here
Q568L4 View 3D Structure Click here
Q5JN09 View 3D Structure Click here
Q5M9G0 View 3D Structure Click here
Q5RIV4 View 3D Structure Click here
Q5U3U4 View 3D Structure Click here
Q5U3U4 View 3D Structure Click here
Q5XIE7 View 3D Structure Click here
Q6ERC2 View 3D Structure Click here
Q6IDB6 View 3D Structure Click here
Q6P0R4 View 3D Structure Click here
Q6P6J0 View 3D Structure Click here
Q6PAT0 View 3D Structure Click here
Q75LI1 View 3D Structure Click here
Q7K157 View 3D Structure Click here
Q7KTJ2 View 3D Structure Click here
Q7Z6V5 View 3D Structure Click here
Q86JM0 View 3D Structure Click here
Q8BMD5 View 3D Structure Click here
Q8BMD5 View 3D Structure Click here
Q8GWP5 View 3D Structure Click here
Q8I5Z9 View 3D Structure Click here
Q8IDK5 View 3D Structure Click here
Q8JFW4 View 3D Structure Click here
Q8K2D6 View 3D Structure Click here
Q8S0I1 View 3D Structure Click here
Q8T1Z7 View 3D Structure Click here
Q95QD6 View 3D Structure Click here
Q95Y87 View 3D Structure Click here
Q96EY9 View 3D Structure Click here
Q9BWV3 View 3D Structure Click here
Q9BWV3 View 3D Structure Click here
Q9NAH8 View 3D Structure Click here
Q9P7N4 View 3D Structure Click here
Q9S847 View 3D Structure Click here
Q9STY4 View 3D Structure Click here
Q9SU86 View 3D Structure Click here
Q9SU87 View 3D Structure Click here
Q9URQ3 View 3D Structure Click here
Q9VEM0 View 3D Structure Click here
Q9VLR2 View 3D Structure Click here
Q9VLR3 View 3D Structure Click here
Q9VWA2 View 3D Structure Click here
Q9XEX4 View 3D Structure Click here
Q9XXD0 View 3D Structure Click here