Summary: MafB19-like deaminase
MafB19-like deaminase Provide feedback
A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Neisseria MafB19 . Members of this family are present in a wide phyletic range of bacteria and are predicted to function as toxins in bacterial polymorphic toxin systems .
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_N Bd3614-deam dCMP_cyt_deam_1 Ldh_2 XOO_2897-deam|
|Similarity to PfamA using HHSearch:||dCMP_cyt_deam_1 Bd3614-deam|
This tab holds annotation information from the InterPro database.
InterPro entry IPR028883tRNA-specific adenosine deaminase catalyses the deamination of adenosine to inosine at the wobble position 34 of tRNA(Arg2) [PUBMED:12110595, PUBMED:16700551, PUBMED:17554781, PUBMED:16142903].
|Molecular function||tRNA-specific adenosine deaminase activity (GO:0008251)|
|Biological process||tRNA wobble adenosine to inosine editing (GO:0002100)|
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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
|Author:||Iyer LM, Zhang D, Aravind L|
|Number in seed:||10|
|Number in full:||3839|
|Average length of the domain:||143.90 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||76.53 %|
|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:||5|
|Download:||download the raw HMM for this family|
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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 MafB19-deam domain has been found. There are 12 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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