Protein Family Models

Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding [1] [2]. [1]. 16996291. Structural basis for processivity and single-strand specificity. of RNase II.. Zuo Y, Vincent HA, Zhang J, Wang Y, Deutscher MP, Malhotra A;. Mol Cell. 2006;24:149-156.. [2]. 16957732. Unravelling the dynamics of RNA degradation by ribonuclease II. and its RNA-bound complex.. Frazao C, McVey CE, Amblar M, Barbas A, Vonrhein C, Arraiano CM,. Carrondo MA;. Nature. 2006;443:110-114. (from Pfam)

Date:

2024-08-14

This domain has an OB fold and is found in the Dis3l2 protein [1]. This domain along with CSD1 binds to RNA. [1]. 25119025. Mechanism of Dis3l2 substrate recognition in the Lin28-let-7. pathway.. Faehnle CR, Walleshauser J, Joshua-Tor L;. Nature. 2014;514:252-256.. [2]. 18374646. Structure of the active subunit of the yeast exosome core,. Rrp44: diverse modes of substrate recruitment in the RNase II. nuclease family.. Lorentzen E, Basquin J, Tomecki R, Dziembowski A, Conti E;. Mol Cell. 2008;29:717-728.. [3]. 19879841. The yeast exosome functions as a macromolecular cage to channel. RNA substrates for degradation.. Bonneau F, Basquin J, Ebert J, Lorentzen E, Conti E;. Cell. 2009;139:547-559.. [4]. 23376952. Crystal structure of an RNA-bound 11-subunit eukaryotic exosome. complex.. Makino DL, Baumgartner M, Conti E;. Nature. 2013;495:70-75. (from Pfam)

Date:

2024-08-14

This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies. (from Pfam)

Date:

2024-08-14

This domain is the catalytic domain of ribonuclease II [1]. [1]. 16806266. Characterization of the functional domains of Escherichia coli. RNase II.. Amblar M, Barbas A, Fialho AM, Arraiano CM;. J Mol Biol. 2006;360:921-933. (from Pfam)

Date:

2024-08-14

The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Structure and an extension of S1 family.. [1]. 9008164. The solution structure of the S1 RNA binding domain: a member of. an ancient nucleic acid-binding fold.. Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG;. Cell 1997;88:235-242. (from Pfam)

Date:

2024-08-14

ribonuclease R (RNaseR or RNR) family protein similar to RNR, a 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs

Date:

2024-05-10

This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.

Gene:

rnr

Date:

2024-05-16

This HMM is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.

Date:

2024-05-17