Protein Family Models

This domain is found in ATP-dependent DNA helicase RecG from bacteria the homologue from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteristic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis [1]. [1]. 11595187. Structural analysis of DNA replication fork reversal by RecG. Singleton MR, Scaife S, Wigley DB;. Cell. 2001;107:79-89. (from Pfam)

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2024-10-16

This DNA-binding domain has an OB-fold with large elaborations [1]. [1]. 11595187. Structural analysis of DNA replication fork reversal by RecG. Singleton MR, Scaife S, Wigley DB;. Cell. 2001;107:79-89. (from Pfam)

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2024-10-16

SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner [1,2]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the Pfam:PF00270 [3]. [1]. 9644254. Amino-terminal region of SecA is involved in the function of SecG for protein translocation into Escherichia coli membrane vesicles. Mori H, Sugiyama H, Yamanaka M, Sato K, Tagaya M, Mizushima S;. J Biochem (Tokyo) 1998;124:122-129. [2]. 2542029. SecA protein hydrolyzes ATP and is an essential component of the protein translocation ATPase of Escherichia coli. Lill R, Cunningham K, Brundage LA, Ito K, Oliver D, Wickner W;. EMBO J 1989;8:961-966. [3]. 12242434. Nucleotide control of interdomain interactions in the conformational reaction cycle of SecA. Hunt JF, Weinkauf S, Henry L, Fak JJ, McNicholas P, Oliver DB, Deisenhofer J;. Science 2002;297:2018-2026. (from Pfam)

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2024-10-16

Date:

2024-08-14

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)

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2024-10-16

Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. [1]. 10322435. Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. de la Cruz J, Kressler D, Linder P;. Trends Biochem Sci 1999;24:192-198. [2]. 9862990. The DEAD box RNA helicase family in Arabidopsis thaliana. Aubourg S, Kreis M, Lecharny A;. Nucleic Acids Res 1999;27:628-636. (from Pfam)

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2024-10-16

The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. (from Pfam)

Date:

2024-08-14