The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...
The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...
The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.
SF3A2 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp2 ...
SF3A2 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp21 (subunit 1). with Prp21 wrapping around Prp11 [1].
This family of proteins the superfamily of PHD-finger proteins. At least one example, from mouse, may act as a chromatin-associated protein[1]. The S. pombe ini1 gene is essential, required for splicing [2]. It is localised in the nucleus, but not de ...
This family of proteins the superfamily of PHD-finger proteins. At least one example, from mouse, may act as a chromatin-associated protein[1]. The S. pombe ini1 gene is essential, required for splicing [2]. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 [2].
The helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain [1,2,3]. These domains collaborate wit ...
The helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain [1,2,3]. These domains collaborate with RecA domains at the N-terminal in completing an RNA binding channel to allow the helicases to keep a stable grip on the RNA [3] and assure its correct function. This entry represents the WH domain, which connects the N- (RecA domains) and C-terminal domains (ratchet-like and OB-fold) of helicases.
This family is found towards the C-terminus of the DEAD-box helicases (Pfam:PF00270). In these helicases it is apparently always found in association with Pfam:PF04408. There do seem to be a couple of instances where it occurs by itself - e.g. Swiss: ...
This family is found towards the C-terminus of the DEAD-box helicases (Pfam:PF00270). In these helicases it is apparently always found in association with Pfam:PF04408. There do seem to be a couple of instances where it occurs by itself - e.g. Swiss:Q84VZ2. The structure PDB:3i4u adopts an OB-fold. helicases (Pfam:PF00270). In these helicases it is apparently always found in association with Pfam:PF04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins [1].
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 ...
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.
The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
The helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain (Pfam:PF04408) and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain [1,2,3]. These domains c ...
The helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain (Pfam:PF04408) and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain [1,2,3]. These domains collaborate with the RecA domains at the N-terminal in completing an RNA binding channel to allow the helicases to keep a stable grip on the RNA [3]. This entry represents the ratchet-like domain, which may be important for RNA translocation [1,2].
Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
SF3A3 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp2 ...
SF3A3 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp21 (subunit 1). Prp9 and Prp21 were not thought to interact with each other but the alpha1 helix of Prp9 does make important contacts with the SURP2 domain of Prp21, thus the two do interact via a bidentate-binding mode. Prp9 harbours a major binding site for stem-loop IIa of U2 snRNA [1].
This domain represents the C-terminal region of the Replication stress response SDE2, a genome surveillance factor. It contains the DNA-binding SAP domain, frequently found in proteins involved in DNA repair. SDE2 C-terminal domain must be cleaved fr ...
This domain represents the C-terminal region of the Replication stress response SDE2, a genome surveillance factor. It contains the DNA-binding SAP domain, frequently found in proteins involved in DNA repair. SDE2 C-terminal domain must be cleaved from its N-terminal at a diglycine motif within the ubiquitin-like fold, after Proliferating cell nuclear antigen (PCNA) interaction. This generates a functional protein that negatively regulates damage-inducible PCNA monoubiquitination, which then is proteolytically degraded to allow S phase progression and replication fork recovery in response to DNA damage [1].
This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is th ...
This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription.
This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding [1].
