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The AID/APOBEC family of nucleic acid mutators.

Conticello SG - Genome Biol. (2008)

Bottom Line: The AID/APOBECs, a group of cytidine deaminases, represent a somewhat unusual protein family that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to uridine.APOBEC1 edits the mRNA for apolipoprotein B, a protein involved in lipid transport.A detailed understanding of the biological roles of the family is still some way off, however, and the functions of some members of the family are completely unknown.

View Article: PubMed Central - HTML - PubMed

Affiliation: Core Research Laboratory, Istituto Toscano Tumori, Florence, Via Cosimo il Vecchio 2, 50139 Firenze, Italy. silvo.conticello@ittumori.it

ABSTRACT
The AID/APOBECs, a group of cytidine deaminases, represent a somewhat unusual protein family that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to uridine. The ancestral AID/APOBECs originated from a branch of the zinc-dependent deaminase superfamily at the beginning of the vertebrate radiation. Other members of the family have arisen in mammals and present a history of complex gene duplications and positive selection. All AID/APOBECs have a characteristic zinc-coordination motif, which forms the core of the catalytic site. The crystal structure of human APOBEC2 shows remarkable similarities to that of the bacterial tRNA-editing enzyme TadA, which suggests a conserved mechanism by which polynucleotides are recognized and deaminated. The AID/APOBECs seem to have diverse roles. AID and the APOBEC3s are DNA mutators, acting in antigen-driven antibody diversification processes and in an innate defense system against retroviruses, respectively. APOBEC1 edits the mRNA for apolipoprotein B, a protein involved in lipid transport. A detailed understanding of the biological roles of the family is still some way off, however, and the functions of some members of the family are completely unknown. Given their ability to mutate DNA, a role for the AID/APOBECs in the onset of cancer has been proposed.

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Logo alignment of the exon encoding the zinc-coordinating motif in the AID, APOBEC1, APOBEC3, and APOBEC2 clusters. The height of the letter represents the conservation of that given residue. The zinc-coordinating H [AV]E-x(24-36)-PCxxC motif is labeled. The secondary structure, predicted from the APOBEC2 structure, is shown below the alignment. The α helices are shown as cylinders and the β-strands as arrows. α Helices 2 and 3, providing the scaffold for the catalytic core, are labeled in blue. The conserved loops that might have a role in substrate recognition are color-coded (pink and orange) and indicated by arrows. The Logo alignment was generated using WebLogo [110] on a subset of the alignment provided as Additional data file 1 in which APOBEC4 and outgroup sequences were excluded.
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Figure 3: Logo alignment of the exon encoding the zinc-coordinating motif in the AID, APOBEC1, APOBEC3, and APOBEC2 clusters. The height of the letter represents the conservation of that given residue. The zinc-coordinating H [AV]E-x(24-36)-PCxxC motif is labeled. The secondary structure, predicted from the APOBEC2 structure, is shown below the alignment. The α helices are shown as cylinders and the β-strands as arrows. α Helices 2 and 3, providing the scaffold for the catalytic core, are labeled in blue. The conserved loops that might have a role in substrate recognition are color-coded (pink and orange) and indicated by arrows. The Logo alignment was generated using WebLogo [110] on a subset of the alignment provided as Additional data file 1 in which APOBEC4 and outgroup sequences were excluded.

Mentions: Like all zinc-dependent deaminases, the main structural feature of the AID/APOBECs is the domain responsible for their catalytic activity. In the amino-acid sequence, the signature for this domain is a H [AV]E-x[24-36]-PCxxC motif (where x is any amino acid) (Figure 3). The histidine (H) and the two cysteines (C) coordinate a zinc atom and form the catalytic core of the deaminase (Figure 4). The cytidine is bound in this pocket and is deaminated through nucleophilic attack on the ammonium group on its carbon 4 by an activated water molecule (coordinated by the zinc atom) and the nearby glutamate, which acts as a proton donor.


The AID/APOBEC family of nucleic acid mutators.

Conticello SG - Genome Biol. (2008)

Logo alignment of the exon encoding the zinc-coordinating motif in the AID, APOBEC1, APOBEC3, and APOBEC2 clusters. The height of the letter represents the conservation of that given residue. The zinc-coordinating H [AV]E-x(24-36)-PCxxC motif is labeled. The secondary structure, predicted from the APOBEC2 structure, is shown below the alignment. The α helices are shown as cylinders and the β-strands as arrows. α Helices 2 and 3, providing the scaffold for the catalytic core, are labeled in blue. The conserved loops that might have a role in substrate recognition are color-coded (pink and orange) and indicated by arrows. The Logo alignment was generated using WebLogo [110] on a subset of the alignment provided as Additional data file 1 in which APOBEC4 and outgroup sequences were excluded.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2481415&req=5

Figure 3: Logo alignment of the exon encoding the zinc-coordinating motif in the AID, APOBEC1, APOBEC3, and APOBEC2 clusters. The height of the letter represents the conservation of that given residue. The zinc-coordinating H [AV]E-x(24-36)-PCxxC motif is labeled. The secondary structure, predicted from the APOBEC2 structure, is shown below the alignment. The α helices are shown as cylinders and the β-strands as arrows. α Helices 2 and 3, providing the scaffold for the catalytic core, are labeled in blue. The conserved loops that might have a role in substrate recognition are color-coded (pink and orange) and indicated by arrows. The Logo alignment was generated using WebLogo [110] on a subset of the alignment provided as Additional data file 1 in which APOBEC4 and outgroup sequences were excluded.
Mentions: Like all zinc-dependent deaminases, the main structural feature of the AID/APOBECs is the domain responsible for their catalytic activity. In the amino-acid sequence, the signature for this domain is a H [AV]E-x[24-36]-PCxxC motif (where x is any amino acid) (Figure 3). The histidine (H) and the two cysteines (C) coordinate a zinc atom and form the catalytic core of the deaminase (Figure 4). The cytidine is bound in this pocket and is deaminated through nucleophilic attack on the ammonium group on its carbon 4 by an activated water molecule (coordinated by the zinc atom) and the nearby glutamate, which acts as a proton donor.

Bottom Line: The AID/APOBECs, a group of cytidine deaminases, represent a somewhat unusual protein family that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to uridine.APOBEC1 edits the mRNA for apolipoprotein B, a protein involved in lipid transport.A detailed understanding of the biological roles of the family is still some way off, however, and the functions of some members of the family are completely unknown.

View Article: PubMed Central - HTML - PubMed

Affiliation: Core Research Laboratory, Istituto Toscano Tumori, Florence, Via Cosimo il Vecchio 2, 50139 Firenze, Italy. silvo.conticello@ittumori.it

ABSTRACT
The AID/APOBECs, a group of cytidine deaminases, represent a somewhat unusual protein family that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to uridine. The ancestral AID/APOBECs originated from a branch of the zinc-dependent deaminase superfamily at the beginning of the vertebrate radiation. Other members of the family have arisen in mammals and present a history of complex gene duplications and positive selection. All AID/APOBECs have a characteristic zinc-coordination motif, which forms the core of the catalytic site. The crystal structure of human APOBEC2 shows remarkable similarities to that of the bacterial tRNA-editing enzyme TadA, which suggests a conserved mechanism by which polynucleotides are recognized and deaminated. The AID/APOBECs seem to have diverse roles. AID and the APOBEC3s are DNA mutators, acting in antigen-driven antibody diversification processes and in an innate defense system against retroviruses, respectively. APOBEC1 edits the mRNA for apolipoprotein B, a protein involved in lipid transport. A detailed understanding of the biological roles of the family is still some way off, however, and the functions of some members of the family are completely unknown. Given their ability to mutate DNA, a role for the AID/APOBECs in the onset of cancer has been proposed.

Show MeSH
Related in: MedlinePlus