Summary: APOBEC-like N-terminal domain
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APOBEC Edit Wikipedia article
|APOBEC-like N-terminal domain|
|APOBEC-like C-terminal domain|
APOBEC ("apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like") is a family of evolutionarily conserved cytidine deaminases.
A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalytic domain. More specifically, the catalytic domain is a zinc dependent cytidine deaminase domain and is essential for cytidine deamination. RNA editing by APOBEC-1 requires homodimerisation and this complex interacts with RNA binding proteins to form the editosome.
Human genes encoding members of the APOBEC protein family include:
- APOBEC3D ("APOBEC3E" now refers to this)
- Activation-induced (cytidine) deaminase
- PMID 17187054. doi:10.1038/nature05492.; rendered using PyMOL.; Prochnow, C.; Bransteitter, R.; Klein, M.G.; Goodman, M.F.; Chen, X.S.; functional implications for the deaminase AID. (2007). "The APOBEC-2 crystal structure". Nature. 445 (7126): 447–451.
- Wedekind JE, Dance GS, Sowden MP, Smith HC (April 2003). "Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business". Trends Genet. 19 (4): 207–16. PMID 12683974. doi:10.1016/S0168-9525(03)00054-4.
- Unexpected DNA-Binding Mechanism Suggests Ways to Block Enzyme Activity in Cancer
- Jaguva Vasudevan, AA; Smits SH; Höppner A; Häussinger D; Koenig BW; Münk C. (June 2013). "Structural features of antiviral DNA cytidine deaminases". Biol Chem. 394 (11): 1357–1370. PMID 23787464. doi:10.1515/hsz-2013-0165.
|This protein-related article is a stub. You can help Wikipedia by expanding it.|
APOBEC-like N-terminal domain Provide feedback
A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain. RNA editing by APOBEC-1 requires homodimerisation and this complex interacts with RNA binding proteins to from the editosome  (and references therein). This family also includes the functionally homologous activation induced deaminase (AID), which is essential for the development of antibody diversity in B lymphocytes, and the sea lamprey PmCDA1 and PmCDA2, which are predicted to play an AID-like role in the adaptive immune response of jawless vertebrates . Divergent members of this family are present in various eukaryotes such as Nematostella, C. elegans, Micromonas and Emiliania, and prokaryotes such as Wolbachia and Pseudomonas brassicacearum .
Wedekind JE, Dance GS, Sowden MP, Smith HC; , Trends Genet 2003;19:207-216.: Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business. PUBMED:12683974 EPMC:12683974
Rogozin IB, Iyer LM, Liang L, Glazko GV, Liston VG, Pavlov YI, Aravind L, Pancer Z;, Nat Immunol. 2007;8:647-656.: Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase. PUBMED:17468760 EPMC:17468760
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
Internal database links
|SCOOP:||APOBEC_C dCMP_cyt_deam_1 MafB19-deam Toxin-deaminase|
|Similarity to PfamA using HHSearch:||APOBEC_C|
This tab holds annotation information from the InterPro database.
InterPro entry IPR013158
This domain is found at the N terminus of the Apolipoprotein B mRNA editing enzyme. Apobec-1 catalyzes C to U editing of apolipoprotein B (apoB) mRNA in the mammalian intestine.
The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination. APOBEC-3 like members contain two copies of this domain. This family also includes the functionally homologous activation induced deaminase, which is essential for the development of antibody diversity in B lymphocytes. RNA editing by APOBEC-1 requires homodimerisation and this complex interacts with RNA binding proteins to from the editosome [PUBMED:12683974] (and references therein).
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|
|zinc ion binding (GO:0008270)|
- the number of sequences which exhibit this architecture
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This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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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 . 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 18 members:A_deamin AICARFT_IMPCHas APOBEC_C APOBEC_N Bd3614-deam dCMP_cyt_deam_1 dCMP_cyt_deam_2 DYW_deaminase FdhD-NarQ LmjF365940-deam MafB19-deam OTT_1508_deam Pput2613-deam SCP1201-deam TM1506 Toxin-deaminase XOO_2897-deam YwqJ-deaminase
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Number in seed:||27|
|Number in full:||596|
|Average length of the domain:||160.90 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||57.54 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 APOBEC_N domain has been found. There are 38 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 seqence.
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