Protein Family Models

The HHH domain is a short DNA-binding domain [1]. [1]. 8692686. The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Doherty AJ, Serpell LC, Ponting CP;. Nucleic Acids Res 1996;24:2488-2497. (from Pfam)

Date:

2024-10-16

This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family [2,3]. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain. [1]. 2047877. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D;. Science 1991;252:1682-1689. [2]. 7760808. Rpa4, a homolog of the 34-kilodalton subunit of the replication protein A complex. Keshav KF, Chen C, Dutta A;. Mol Cell Biol 1995;15:3119-3128. [3]. 8990123. Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L;. Nature 1997;385:176-181. [4]. 10829230. Protein fold recognition using sequence profiles and its application in structural genomics. Koonin EV, Wolf YI, Aravind L;. Adv Protein Chem 2000;54:245-275. (from Pfam)

Date:

2024-10-16

Date:

2020-10-26

This HMM represents the well-conserved C-terminal region of a large number of inteins. It is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. Inteins are regions encoded within proteins from which they remove themselves after translation in a self-splicing reaction, leaving the remainder of the coding region to form a complete, functional protein as if the intein were never there. Proteins with inteins include RecA, GyrA, ribonucleotide reductase, and others. Most inteins have a central region with putative endonuclease activity.

Date:

2021-04-27

PRK07373 family protein

Date:

2017-03-02