Protein Family Models

Ribonuclease J1, as the term is used in Staphylococcus aureus, is one of two RNase J paralogs that are about 40 percent identical.

Gene:

rnjA

Date:

2024-08-03

This domain is found at the C-terminus of Ribonuclease J proteins. Its function is unknown, but deletion of this domain causes dissociation to monomers [2]. [1]. 21893286. Molecular basis for the recognition and cleavage of RNA by the bifunctional 5'-3' exo/endoribonuclease RNase J. Dorleans A, Li de la Sierra-Gallay I, Piton J, Zig L, Gilet L, Putzer H, Condon C;. Structure. 2011;19:1252-1261. [2]. 18204464. Structural insights into the dual activity of RNase J. Li de la Sierra-Gallay I, Zig L, Jamalli A, Putzer H;. Nat Struct Mol Biol. 2008;15:206-212. (from Pfam)

Date:

2024-10-16

This domain is found in Ribonuclease J from Thermus thermophilus (RNaseJ) and similar bacterial proteins. RNaseJ is an RNase that has endonuclease and possibly 5'-3' exonuclease activity. It is probably involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay. This protein shows three globular domains: the beta lactamase core (formed by two separate regions, Pfam:PF12706 and Pfam:PF07521), the beta-CASP (this entry) and the C-terminal domain (Pfam: PF17770). This domain consists of a central five-stranded parallel beta-sheet that is surrounded by five alpha-helices [1,2]. Paper describing PDB structure 3bk1. [1]. 18204464. Structural insights into the dual activity of RNase J. Li de la Sierra-Gallay I, Zig L, Jamalli A, Putzer H;. Nat Struct Mol Biol. 2008;15:206-212. Paper describing PDB structure 3t3n. [2]. 21893286. Molecular basis for the recognition and cleavage of RNA by the bifunctional 5'-3' exo/endoribonuclease RNase J. Dorleans A, Li de la Sierra-Gallay I, Piton J, Zig L, Gilet L, Putzer H, Condon C;. Structure. 2011;19:1252-1261. Paper describing PDB structure 3zq4. [3]. 21893285. Unusual, dual endo- and exonuclease activity in the degradosome explained by crystal structure analysis of RNase J1. Newman JA, Hewitt L, Rodrigues C, Solovyova A, Harwood CR, Lewis RJ;. Structure. 2011;19:1241-1251. Paper describing PDB structure 4xwt. [4]. 25940620. Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J. Zhao Y, Lu M, Zhang H, Hu J, Zhou C, Xu Q, Ul Hussain Shah AM, Xu H, Wang L, Hua Y;. Nucleic Acids Res. 2015;43:5550-5559. Paper describing PDB stru. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

The MBL fold superfamily includes the metallo-beta-lactamases (class B beta-lactamases), but includes also a much larger family of hydrolases that are not beta-lactamases at all. See also the related family PF00753.

Date:

2024-08-14

The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in Pfam:PF00753 and are common to all metallo-beta-lactamases. This, the fifth motif [1], appears to be specific to Zn-dependent metallohydrolases such as ribonuclease J 2 [4] which are involved in the processing of mRNA [2,3]. This domain adds essential structural elements to the CASP-domain and is unique to RNA/DNA-processing nucleases, showing that they are pre-mRNA 3'-end-processing endonucleases [2,3,4]. [1]. 12177301. Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family. Callebaut I, Moshous D, Mornon JP, de Villartay JP;. Nucleic Acids Res 2002;30:3592-3601. [2]. 17128255. Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. Mandel CR, Kaneko S, Zhang H, Gebauer D, Vethantham V, Manley JL, Tong L;. Nature. 2006;444:953-956. [3]. 20544974. Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii. Nishida Y, Ishikawa H, Baba S, Nakagawa N, Kuramitsu S, Masui R;. Proteins. 2010;78:2395-2398. [4]. 21764917. Characterization of components of the Staphylococcus aureus mRNA degradosome holoenzyme-like complex. Roux CM, DeMuth JP, Dunman PM;. J Bacteriol. 2011;193:5520-5526. (from Pfam)

Date:

2024-10-16

Date:

2024-08-14

ribonuclease J plays a key part in RNA processing and in RNA degradation; it can act as an endonuclease which is specific for single-stranded regions of RNA irrespective of their sequence or location, and as a processive 5' exonuclease which only acts on substrates having a single phosphate or a hydroxyl at the 5' end

Date:

2024-05-13

This family of metalloenzymes includes RNase J1 and RNase J2, involved in mRNA degradation in a wide range of organism.

Date:

2024-05-16