Structure of PDB 3oin Chain A

Receptor sequence
>3oinA (length=217) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
PPVLTSKDKITKRMIVVLAMASLETHKIKYVLLNCDDHQGLLKKMGRDIS
EARPDITHQCLLTLLDSPINKAGKLQVYIQTSRGILIEVNPTVRIPRTFK
RFSGLMVQLLHKLSIRSVNSEEKLLKVIKNPITDHLPTKCRKVTLSFDAP
VIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYVDEKVGLSNYPLSAS
VACSKFCHGAEDAWNIL
3D structure
PDB3oin Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.
ChainA
Resolution1.9 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.1.1.260: rRNA small subunit pseudouridine methyltransferase Nep1.
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 rna A R129 P131 R132 T133 K135 R136 G139 L140 Q143 S152 L159 R94 P96 R97 T98 K100 R101 G104 L105 Q108 S117 L124
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0019843 rRNA binding
GO:0042802 identical protein binding
GO:0070037 rRNA (pseudouridine) methyltransferase activity
Biological Process
GO:0000447 endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000472 endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000480 endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing
GO:0030490 maturation of SSU-rRNA
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
GO:0070475 rRNA base methylation
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005880 nuclear microtubule
GO:0030686 90S preribosome
GO:0032040 small-subunit processome
GO:0034399 nuclear periphery
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3oin, PDBe:3oin, PDBj:3oin
PDBsum3oin
PubMed21087996
UniProtQ06287|NEP1_YEAST Ribosomal RNA small subunit methyltransferase NEP1 (Gene Name=EMG1)

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