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391  structures 9505  species 14  interactions 63247  sequences 2487  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 33 families and the total number of domains in the clan is 63247. 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 33 member families:

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

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) 26475 (41.9%) View
AICARFT_IMPCHas (PF01808) 8643 (13.7%) View
DYW_deaminase (PF14432) 8379 (13.2%) View
MafB19-deam (PF14437) 6997 (11.1%) View
FdhD-NarQ (PF02634) 4484 (7.1%) View
A_deamin (PF02137) 2269 (3.6%) View
LpxI_C (PF06230) 1224 (1.9%) View
OTT_1508_deam (PF14441) 1110 (1.8%) View
dCMP_cyt_deam_2 (PF08211) 715 (1.1%) View
Inv-AAD (PF18785) 652 (1.0%) View
YwqJ-deaminase (PF14431) 389 (0.6%) View
XOO_2897-deam (PF14440) 356 (0.6%) View
TM1506 (PF08973) 222 (0.4%) View
APOBEC2 (PF18772) 198 (0.3%) View
SCP1201-deam (PF14428) 149 (0.2%) View
Toxin-deaminase (PF14424) 143 (0.2%) View
NAD1 (PF18778) 142 (0.2%) View
continued
Pfam family Num. domains Alignment
APOBEC_N (PF08210) 135 (0.2%) View
NAD2 (PF18782) 119 (0.2%) View
APOBEC_C (PF05240) 87 (0.1%) View
SNAD4 (PF18750) 84 (0.1%) View
LmjF365940-deam (PF14421) 75 (0.1%) View
APOBEC4 (PF18775) 52 (0.1%) View
APOBEC4_like (PF18774) 33 (0.1%) View
APOBEC3 (PF18771) 21 (0.0%) View
SNAD1 (PF18744) 18 (0.0%) View
APOBEC1 (PF18769) 16 (0.0%) View
Pput2613-deam (PF14427) 14 (0.0%) View
AID (PF18767) 13 (0.0%) View
DAAD (PF18752) 13 (0.0%) View
Bd3614-deam (PF14439) 10 (0.0%) View
SNAD3 (PF18749) 5 (0.0%) View
SNAD2 (PF18745) 5 (0.0%) View
Total: 33 Total: 63247 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 14 interactions for this clan. More...

Interacting families
A B
A_deamin A_deamin
AICARFT_IMPCHas AICARFT_IMPCHas
MGS
APOBEC_C APOBEC_C
APOBEC_N APOBEC_N
dCMP_cyt_deam_1 dCMP_cyt_deam_1
dCMP_cyt_deam_2
RibD_C
THUMP
dCMP_cyt_deam_2 dCMP_cyt_deam_1
dCMP_cyt_deam_2
FdhD-NarQ FdhD-NarQ
MGS AICARFT_IMPCHas
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 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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