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208  structures 5319  species 12  interactions 27014  sequences 1010  architectures

Clan: CDA (CL0109)

Summary

Cytidine deaminase-like (CDA) superfamily Add an annotation

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.

This clan contains 16 families and the total number of domains in the clan is 27014. The clan was built by RD FinnL CoinLM IyerD Zhang and L Aravind.

Literature references

  1. Liaw SH, Chang YJ, Lai CT, Chang HC, Chang GG; , J Biol Chem 2004;279:35479-35485.: Crystal structure of Bacillus subtilis guanine deaminase: the first domain-swapped structure in the cytidine deaminase superfamily. PUBMED:15180998 EPMC:15180998
  2. Iyer LM, Zhang D, Rogozin IB, Aravind L;, Nucleic Acids Res. 2011; [Epub ahead of print]: Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. PUBMED:21890906 EPMC:21890906

Members

This clan contains the following 16 member families:

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

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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Alignments

The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
dCMP_cyt_deam_1 (PF00383) 17292 (64.0%) View
AICARFT_IMPCHas (PF01808) 4880 (18.1%) View
DYW_deaminase (PF14432) 1779 (6.6%) View
dCMP_cyt_deam_2 (PF08211) 900 (3.3%) View
A_deamin (PF02137) 781 (2.9%) View
APOBEC_N (PF08210) 683 (2.5%) View
OTT_1508_deam (PF14441) 207 (0.8%) View
Toxin-deaminase (PF14424) 120 (0.4%) View
YwqJ-deaminase (PF14431) 91 (0.3%) View
APOBEC_C (PF05240) 86 (0.3%) View
MafB19-deam (PF14437) 53 (0.2%) View
XOO_2897-deam (PF14440) 52 (0.2%) View
SCP1201-deam (PF14428) 44 (0.2%) View
LmjF365940-deam (PF14421) 36 (0.1%) View
Pput2613-deam (PF14427) 6 (0.0%) View
Bd3614-deam (PF14439) 4 (0.0%) View
Total: 16 Total: 27014 Clan alignment
 

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Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

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This tree shows the occurrence of the domains in this clan across different species. More...

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Interactions

There are 12 interactions for this clan. More...

Interacting families
A B
dCMP_cyt_deam_2 dCMP_cyt_deam_1
dCMP_cyt_deam_2
A_deamin A_deamin
APOBEC_N APOBEC_C
APOBEC_N
dCMP_cyt_deam_1 dCMP_cyt_deam_1
RibD_C
dCMP_cyt_deam_2
AICARFT_IMPCHas AICARFT_IMPCHas
MGS
APOBEC_C APOBEC_C
APOBEC_N

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 MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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