Protein Family Models

This is one of two Tudor-like domains found in the N-terminal region of RapA proteins. RapA is an abundant RNAP-associated protein of 110-kDa molecular weight with ATPase activity. It forms a stable complex with the RNAP core enzyme, but not with the holoenzyme. The ATPase activity of RapA increases upon its binding to RNAP [1]. The N-terminal region of RapA contains two copies of a Tudor-like domains, both folded as a highly bent antiparallel beta-sheet. This fold is also found in transcription factor NusG , ribosomal protein L24, human SMN (survival of motor neuron) protein, mammalian DNA repair factor 53BP1, putative fission yeast DNA repair factor Crb2 and bacterial transcription-repair coupling factor known as Mfd. The functional roles of the N-terminal region homologs in these proteins suggest that the Tudor-like domains of RapA may interact with both nucleic acids and RNAP [2]. [1]. 25646438. Structural basis for transcription reactivation by RapA.. Liu B, Zuo Y, Steitz TA;. Proc Natl Acad Sci U S A. 2015;112:2006-2010.. [2]. 18786404. Structure of RapA, a Swi2/Snf2 protein that recycles RNA. polymerase during transcription.. Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak. A, Jin DJ, Ji X;. Structure. 2008;16:1417-1427. (from Pfam)

Date:

2024-08-14

This is one of two Tudor-like domains found in the N-terminal region of RapA proteins. RapA is an abundant RNAP-associated protein of 110-kDa molecular weight with ATPase activity. It forms a stable complex with the RNAP core enzyme, but not with the holoenzyme. The ATPase activity of RapA increases upon its binding to RNAP [1]. The N-terminal region of RapA contains two copies of a Tudor-like domains, both folded as a highly bent antiparallel beta-sheet. This fold is also found in transcription factor NusG , ribosomal protein L24, human SMN (survival of motor neuron) protein, mammalian DNA repair factor 53BP1, putative fission yeast DNA repair factor Crb2 and bacterial transcription-repair coupling factor known as Mfd. The functional roles of the N-terminal region homologs in these proteins suggest that the Tudor-like domains of RapA may interact with both nucleic acids and RNAP [2]. [1]. 25646438. Structural basis for transcription reactivation by RapA.. Liu B, Zuo Y, Steitz TA;. Proc Natl Acad Sci U S A. 2015;112:2006-2010.. [2]. 18786404. Structure of RapA, a Swi2/Snf2 protein that recycles RNA. polymerase during transcription.. Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak. A, Jin DJ, Ji X;. Structure. 2008;16:1417-1427. (from Pfam)

Date:

2024-08-14

This domain is found in bacteria. This domain is about 360 amino acids in length. This domain is found associated with Pfam:PF00271, Pfam:PF00176. The function of this domain is not known, but structurally it forms an alpha-beta fold in nature with a central beta-sheet flanked by helices and loops, the beta-sheet being mainly antiparallel and flanked by four alpha helices, among which the two longer helices exhibit a coiled-coil arrangement. [1]. 18786404. Structure of RapA, a Swi2/Snf2 protein that recycles RNA. polymerase during transcription.. Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak. A, Jin DJ, Ji X;. Structure. 2008;16:1417-1427. (from Pfam)

Date:

2024-08-14

Date:

2024-08-14

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)

Date:

2024-08-14

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

This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1)[1,2,3]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. [1]. 7651832. Evolution of the SNF2 family of proteins: subfamilies with. distinct sequences and functions.. Eisen JA, Sweder KS, Hanawalt PC;. Nucleic Acids Res. 1995;23:2715-2723.. [2]. 14729263. The SNF2 domain protein family in higher vertebrates displays. dynamic expression patterns in Xenopus laevis embryos.. Linder B, Cabot RA, Schwickert T, Rupp RA;. Gene. 2004;326:59-66.. [3]. 21549307. Maintenance of silent chromatin through replication requires. SWI/SNF-like chromatin remodeler SMARCAD1.. Rowbotham SP, Barki L, Neves-Costa A, Santos F, Dean W, Hawkes. N, Choudhary P, Will WR, Webster J, Oxley D, Green CM,. Varga-Weisz P, Mermoud JE;. Mol Cell. 2011;42:285-296. (from Pfam)

Date:

2024-08-14