Structure of PDB 5c0y Chain B

Receptor sequence
>5c0yB (length=388) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
KRVEKPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDENNP
SHYPHPYEYEIDHQEYSPEILQIREEIPSKSWDDSVPIWVDTSTELESML
EDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHI
LNEVFTNPSIVKVFHGAFMNIIWLQRDLGLYVVGLFDTYHASKAIGLPRH
SLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAYARADTHFLLNIYDQL
RNKLIESNKLAGVLYESRNVAKRRFEYSKYRPLTPSSEVYSPIKESPWKI
LMYQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTP
TDVIGVVSLTNGVTEHVRQNAKLLANLIRDALRNIKNT
3D structure
PDB5c0y RNA degradation paths in a 12-subunit nuclear exosome complex.
ChainB
Resolution2.1 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D238 E240 N296 Y361 D365
Catalytic site (residue number reindexed from 1) D112 E114 N170 Y235 D239
Enzyme Commision number 3.1.13.-
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 B E240 H241 Y244 H291 F294 Y315 H326 S327 L328 Q345 R399 S413 I419 R461 E114 H115 Y118 H165 F168 Y189 H200 S201 L202 Q219 R273 S287 I293 R334
BS02 MG B D238 L239 E240 D365 D112 L113 E114 D239
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000175 3'-5'-RNA exonuclease activity
GO:0003676 nucleic acid binding
GO:0008408 3'-5' exonuclease activity
Biological Process
GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006139 nucleobase-containing compound metabolic process
GO:0044237 cellular metabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:5c0y, PDBe:5c0y, PDBj:5c0y
PDBsum5c0y
PubMed26222026
UniProtQ12149|RRP6_YEAST Exosome complex exonuclease RRP6 (Gene Name=RRP6)

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