SMART: Pfam domain Smg4

The domain within your query sequence starts at position 63 and ends at position 224; the E-value for the Smg4_UPF3 domain shown below is 1.4e-54.

TALSKVVLRRLPPGLTKEQLEEQLRPLPAHDYFEVVAADLSLYPHVYSRAYINFRNPDDI
LLFRDRFDGYIFIGNKGLEYPAVVEFAPFQKIAKKKLKKKDAKTGSIEDDPEYKQFLESY
SLEEEKTSASPETLLGEIEAKTRELLARRTTPLLEYIKNRKL

Smg4_UPF3

PFAM accession number:	PF03467
Interpro abstract (IPR005120):	Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants [ (PUBMED:11368911) ]. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [ (PUBMED:12718880) (PUBMED:15048104) ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [ (PUBMED:15004547) ].

PFAM accession number:

PF03467

Interpro abstract (IPR005120):

Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants [ (PUBMED:11368911) ]. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [ (PUBMED:12718880) (PUBMED:15048104) ].

This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [ (PUBMED:15004547) ].

This is a PFAM domain. For full annotation and more information, please see the PFAM entry Smg4_UPF3