Structure of PDB 6wug Chain A

Receptor sequence
>6wugA (length=312) Species: 4896 (Schizosaccharomyces pombe) [Search protein sequence]
MLREFSFYDVPPAHVPPVSEPLEIACYSLSRDRELLLDDSKLSYYYPPPL
FSDLNTGFPNRFHPPKSDPDPISIVKDVLMTKGIQMNSSFLTWRGLITKI
MCAPLDPRNHWETYLVMDPTSGIIMMEERTNQDRMCYWGYKFEAISTLPE
IWDAQDVVPDEQYCSIVKINIGKSKLILAGEVDCIWDKKPENPNLHYVEL
KTSKKYPLENYGMRKKLLKYWAQSFLLGIGRIIIGFRDDNGILIEMKELF
THQIPKMLRPYFKPNDWTPNRLLVVLEHALEWIKQTVKQHPPSTEFTLSY
TGGSKLVLRQII
3D structure
PDB6wug DXO/Rai1 enzymes remove 5'-end FAD and dephospho-CoA caps on RNAs.
ChainA
Resolution1.9 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.6.1.-
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 MG A E150 D201 E239 L240 E143 D183 E199 L200
BS02 UBG A P65 K66 S67 D68 P69 W93 R94 G95 E128 N138 Y147 G198 E199 K241 Q263 P65 K66 S67 D68 P69 W93 R94 G95 E128 N131 Y140 G180 E181 K201 Q223
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0004518 nuclease activity
GO:0005515 protein binding
GO:0019003 GDP binding
GO:0034353 mRNA 5'-diphosphatase activity
GO:0046872 metal ion binding
GO:0110152 RNA NAD+-cap (NAD+-forming) hydrolase activity
GO:0140432 5'-hydroxyl dinucleotide hydrolase activity
GO:1990174 phosphodiesterase decapping endonuclease activity
Biological Process
GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0006397 mRNA processing
GO:0110155 NAD-cap decapping
Cellular Component
GO:0005634 nucleus
GO:0005829 cytosol
GO:0090730 Las1 complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6wug, PDBe:6wug, PDBj:6wug
PDBsum6wug
PubMed32374864
UniProtO13836|DXO_SCHPO Decapping nuclease din1 (Gene Name=din1)

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