Protein Family Models

PF18019 represents a branch of HD domain family that is found primarily as an N-terminal nuclease domain of Cas3 enzymes of CRISPR systems.

Date:

2024-10-16

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

This is the C-temrinal domain of Cas3 proteins. The C-terminal domain (CTD) is shown to completely wrap ssDNA inside the helicase. Deletion of the CTD (aa 819-924) reduced CRISPR interference. It is suggested that the CTD regulates the N-terminal HD nuclease activity by functioning as a substrate filter [1]. [1]. 25132177. Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation. Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD Jr, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A;. Nat Struct Mol Biol. 2014;21:771-777. [2]. 25368186. Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3. Gong B, Shin M, Sun J, Jung CH, Bolt EL, van der Oost J, Kim JS;. Proc Natl Acad Sci U S A. 2014;111:16359-16364. (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

CRISPR/Cas systems are widespread, mobile systems for host defense against invasive elements such as phage. In these systems, Cas3 designates one of the core proteins shared widely by multiple types of CRISPR/Cas system. This HMM represents an HD-like endonuclease that occurs either separately or as the N-terminal region of Cas3, the helicase-containing CRISPR-associated protein.

Date:

2021-04-27

This HMM represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by PF00270 (DEAD/DEAH box helicase) and PF00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (PF01966) that is not included within this model.

Gene:

cas3

Date:

2021-04-27