HMM Summary Page: TIGR02383

FunctionRNA chaperone Hfq
Gene Symbolhfq
Trusted Cutoff61.70
Domain Trusted Cutoff61.70
Noise Cutoff31.15
Domain Noise Cutoff31.15
Isology Typeequivalog
HMM Length61
Mainrole CategoryRegulatory functions
Subrole CategoryOther
Gene Ontology TermGO:0003723: RNA binding molecular_function
GO:0006378: mRNA polyadenylation biological_process
GO:0016070: RNA metabolic process biological_process
AuthorHaft DH
Entry DateNov 29 2004 1:11PM
Last ModifiedFeb 14 2011 3:27PM
CommentThis model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PMID:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
ReferencesDR PFAM; PF01423; LSM domain RN [1] RM 15531892 RT Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. RA Mikulecky PJ, Kaw MK, Brescia CC, Takach JC, Sledjeski DD, Feig AL. RL Nat Struct Mol Biol. 2004 in press RN [2] RM 14561880 RT Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RA Moll I, Afonyushkin T, Vytvytska O, Kaberdin VR, Blasi U. RL RNA. 2003 Nov;9(11):1308-14. DR HAMAP; MF_00436; 258 of 263