Protein Family Models

This entry represents the C-terminal domain of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa (Cas3), a DNA-degradation enzyme that forms part of the CRISPR-Cas bacterial immune system. Cas3 contains a Cas2 domain, an HD nuclease domain (Pfam:PF18019), RecA1, RecA2, a long linker region, and a C-terminal domain (this entry). This domain contains two alpha-helices and two six-stranded beta-blades [6]. Paper describing PDB structure 1gm5. [1]. 11595187. Structural analysis of DNA replication fork reversal by RecG. Singleton MR, Scaife S, Wigley DB;. Cell. 2001;107:79-89. Paper describing PDB structure 1t5i. [2]. 15296731. Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA splicing and mRNA export. Zhao R, Shen J, Green MR, MacMorris M, Blumenthal T;. Structure. 2004;12:1373-1381. Paper describing PDB structure 1wp9. [3]. 15642269. Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing. Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K;. Structure. 2005;13:143-153. Paper describing PDB structure 1yks. [4]. 16051820. Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing. Wu J, Bera AK, Kuhn RJ, Smith JL;. J Virol. 2005;79:10268-10277. Paper describing PDB structure 2bhr. [5]. 16051821. Structure of the Dengue virus helicase/nucleoside triphosphatase catalytic domain at a resolution of 2.4 A. Xu T, Sampath A, Chao A, Wen D, Nanao M, Chene P, Vasudevan SG, Lescar J;. J Virol. 2005;79:10278-10288. [6]. 27455460. Structural basis o. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

Date:

2024-08-14

This RNA binding domain is found at the C-terminus of a number of DEAD helicase proteins [1]. It is sufficient to confer specificity for hairpin 92 of 23S rRNA, which is part of the ribosomal A-site. However, several members of this family lack specificity for 23S rRNA. These can proteins can generally be distinguished by a basic region that extends beyond this domain [Karl Kossen, unpublished data]. [1]. 10481020. Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins. Kossen K, Uhlenbeck OC;. Nucleic Acids Res 1999;27:3811-3820. [2]. 12460566. The carboxy-terminal domain of the DExDH protein YxiN is sufficient to confer specificity for 23S rRNA. Kossen K, Karginov FV, Uhlenbeck OC;. J Mol Biol 2002;324:625-636. (from Pfam)

Date:

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)

Date:

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

Exhibits an RNA-dependent ATPase activity, specifically stimulated by bacterial 23S rRNA

Gene:

dbpA

Date:

2021-07-30

ATP-dependent RNA helicase DbpA is a DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit

Date:

2023-03-14