Protein Family Models

This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility [1]. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity [1]. [1]. 21297639. Structural and biochemical studies of the 5'-->3'. exoribonuclease Xrn1.. Chang JH, Xiang S, Xiang K, Manley JL, Tong L;. Nat Struct Mol Biol. 2011;18:270-276.. [2]. 21362555. Coupled 5' nucleotide recognition and processivity in. Xrn1-mediated mRNA decay.. Jinek M, Coyle SM, Doudna JA;. Mol Cell. 2011;41:600-608. (from Pfam)

Date:

2024-08-14

TNRC6-PABC_bdg is a natively unstructured region on the higher eukaryote TNRC6 subset of GW182 proteins that carries the binding motif for the interaction with Polyadenylate-binding protein 1, PABC. TNRC6 are trinucleotide repeat-containing gene 6 proteins required for miRNA-mediated gene silencing that are localised to the P bodies (processing bodies). P bodies are cytoplasmic mRNP aggregates that are involved in general mRNA translation repression and decay, including nonsense-mediated decay. Thus GW182 proteins are essential for microRNA-mediated translational repression and deadenylation in animal cells being a major component of miRISCs. The interaction motif that binds to PABC is ShNWPPEFHPGVPWKGLQ [1]. This region lies between a Q-rich region and the RRM, or RNA-recognition motif, Pfam:PF13893. [1]. 20098421. Structural insights into the human GW182-PABC interaction in. microRNA-mediated deadenylation.. Jinek M, Fabian MR, Coyle SM, Sonenberg N, Doudna JA;. Nat Struct Mol Biol. 2010;17:238-240. (from Pfam)

Date:

2024-08-14

Exportin-5 mediates the nuclear export of proteins bearing a double-stranded RNA binding domain (dsRBD) and double-stranded RNAs (cargos). Exportin-5 yeast homologue, also known as Msn5, is involved in nuclear import of replication protein A and export of Far1 and transcription factors Swi5, Swi6, Msn2, and Pho4. Its Arabidopsis homologue, HASTY 1, is involved in the nuclear export of microRNAs (miRNAs). Paper describing PDB structure 3a6p. [1]. 19965479. A high-resolution structure of the pre-microRNA nuclear export. machinery.. Okada C, Yamashita E, Lee SJ, Shibata S, Katahira J, Nakagawa A,. Yoneda Y, Tsukihara T;. Science. 2009;326:1275-1279. (from Pfam)

Date:

2024-08-14

This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility [1]. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 Pfam:PF18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment Pfam:PF03159 [1]. [1]. 21297639. Structural and biochemical studies of the 5'-->3'. exoribonuclease Xrn1.. Chang JH, Xiang S, Xiang K, Manley JL, Tong L;. Nat Struct Mol Biol. 2011;18:270-276. (from Pfam)

Date:

2024-08-14

This domain is found in mitochondrial proteins, including FAM210A and B, which contains a transmembrane peptide [1,2,3]. Its function is not clear. FAM210A, a protein essential in maintaining skeletal muscle structure and strength [4], interacts with mitochondrial translation elongation factor EF-Tu and promotes mitochondrial protein expression. In FAM210A, this domain is responsible for binding EF-Tu [3]. FAM210B plays a role in erythroid differentiation and is involved in cell proliferation and tumour cell growth suppression [1,5]. [1]. 28594398. Loss of the novel mitochondrial protein FAM210B promotes. metastasis via PDK4-dependent metabolic reprogramming.. Sun S, Liu J, Zhao M, Han Y, Chen P, Mo Q, Wang B, Chen G, Fang. Y, Tian Y, Zhou J, Ma D, Gao Q, Wu P;. Cell Death Dis. 2017;8:e2870.. [2]. 33304386. A Multi-Network Comparative Analysis of Transcriptome and. Translatome Identifies Novel Hub Genes in Cardiac Remodeling.. Boileau E, Doroudgar S, Riechert E, Jurgensen L, Ho TC, Katus. HA, Volkers M, Dieterich C;. Front Genet. 2020;11:583124.. [3]. 33369227. MicroRNA-574 regulates FAM210A expression and influences. pathological cardiac remodeling.. Wu J, Venkata Subbaiah KC, Jiang F, Hedaya O, Mohan A, Yang T,. Welle K, Ghaemmaghami S, Tang WHW, Small E, Yan C, Yao P;. EMBO Mol Med. 2021;13:e12710.. [4]. 29618611. FAM210A is a novel determinant of bone and muscle structure and. strength.. Tanaka KI, Xue Y, Nguyen-Yamamoto L, Morris JA, Kanazawa I,. Sugimoto T, Wing SS, Richards JB, Goltzman D;. Proc Natl Acad Sci U S A. 2018;115:E3759.. [5]. 26968549. Identification of a novel putative mitochondrial protein FAM210B. as. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer [1,2]. It is a divergent double stranded RNA-binding domain [3]. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity [4]. This domain has weak dsRNA-binding activity. It mediates heterodimerisation of Dicer proteins with their respective protein partners [4]. [1]. 16424907. The role of PACT in the RNA silencing pathway.. Lee Y, Hur I, Park SY, Kim YK, Suh MR, Kim VN;. EMBO J. 2006;25:522-532.. [2]. 17666393. Functional anatomy of the Drosophila microRNA-generating enzyme.. Ye X, Paroo Z, Liu Q;. J Biol Chem. 2007;282:28373-28378.. [3]. 16954143. DUF283 domain of Dicer proteins has a double-stranded. RNA-binding fold.. Dlakic M;. Bioinformatics. 2006;22:2711-2714.. [4]. 20106953. Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals. a noncanonical double-stranded RNA-binding fold for. protein-protein interaction.. Qin H, Chen F, Huan X, Machida S, Song J, Yuan YA;. RNA. 2010;16:474-481. (from Pfam)

Date:

2024-08-14