1UW4


Conserved Protein Domain Family
RRM_like_Smg4_UPF3B

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cd12728: RRM_like_Smg4_UPF3B 
Click on image for an interactive view with Cn3D
RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on chromosome X (Upf3B)
This subgroup corresponds to the RRM-like Smg4_UPF3 domain in Upf3B, also termed regulator of nonsense transcripts 3B, or nonsense mRNA reducing factor 3B, a human ortholog of yeast Upf3p and Caenorhabditis elegans SMG-4. It derives from X-linked gene UPF3B and is required for nonsense-mediated mRNA decay (NMD) in human. Upf3B is a nucleocytoplasmic shuttling protein that associates selectively with spliced beta-globin mRNA in vivo. Like other Upf3 proteins, Upf3B contains nuclear import and export signals, and a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that it may be an RNA binding protein.
Statistics
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PSSM-Id: 410127
Aligned: 5 rows
Threshold Bit Score: 174.716
Created: 8-Sep-2011
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
 
polypeptide
Conserved site includes 86 residues -Click on image for an interactive view with Cn3D
Feature 1:polypeptide substrate binding site [polypeptide binding site]
Evidence:
  • Structure:1UW4; Homo sapiens nonsense mediated decay factor Upf3 in complex with factor Upf2, contacts at 4A.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        ########### ############ ############################# #########################
1UW4_A         1 LSKVVIRRLPPtLTKEQLQEHLQPmPEHDYFEFFSNDTSLYPHMYARAYINFKNqEDIILFRDRFDGYVFLDNKGQEYPA 80  human
AAI58354      36 LSKVVIRRLPPsLTKEQLEEHLQPlPDHDYFEFFSNDSSLFPHMFSRAYINFKSqDDIVLFRDRFDGYVFIDHRGQEYPA 115 western clawed ...
CAG32693      54 LSKVVIRRLPPsLTREQLEEHLQPlPEHDYFEFFANDSSLYPHVFSRAYINFRNqEDIVLFRDRFDGYVFVDHKGQEYAA 133 chicken
XP_006003920  35 LTKVVIRRLPPsLTKEQLEEQLQPiPEHDYFEFFSSDSSLYPHMFSRVYINFKNpEDIVLFRDRLDGYVFIDSRGQEYPA 114 coelacanth
NP_957248     36 MTKIVIRRLPPtLTKEDLEEQLQPlPELDYLEFFSSDTSLFPHLFARAYLNFKNqDDIVLFRDRFDGYVFIDNRGQEYPA 115 zebrafish
Feature 1        #########
1UW4_A        81 IVEFAPFQK 89  human
AAI58354     116 IVEFAPFQK 124 western clawed frog
CAG32693     134 IVEFAPFQK 142 chicken
XP_006003920 115 IVEFAPFQK 123 coelacanth
NP_957248    116 IVEFAPFQK 124 zebrafish

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