Structure of PDB 4oo1 Chain J Binding Site BS01

Receptor Information

>4oo1 Chain J (length=493) Species: 559292 (Saccharomyces cerevisiae S288C)

MVEKPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDENNPS
HYPHPYEYEIDHQEYSPEILQIREEIPSKSWDDSVPIWVDTSTELESMLE
DLKNTKEIAVNLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHIL
NEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLPRHS
LAYLLENFANFKTSKKYQLADWRIRPLSKPMTAYARADTHFLLNIYDQLR
NKLIESNKLAGVLYESRNVAKRRFEYSKYRPLTPSSEVYSPIEKESPWKI
LMYQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTP
TDVIGVVSLTNGVTEHVRQNAKLLANLIRDALRNIKNTNSETKADGILLE
TISVPQIRDVMERFSVLCNSNISKSRAKPVTNSSILLGKILPREEHDIAY
SKDGLPNKVKTEDIRIRAQNFKSALANLEDIIFEIEKPLVVPV

Ligand information

>4oo1 Chain S (length=6)

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......

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4oo1 Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): N238 E240 H241 F294 M295 D296 Y315 K319 S327 L328 Q345
• Binding residue (residue number reindexed from 1): N111 E113 H114 F167 M168 D169 Y188 K192 S200 L201 Q218

Enzymatic activity

• Catalytic site (original residue number in PDB): N238 E240 D296 Y361 D365
• Catalytic site (residue number reindexed from 1): N111 E113 D169 Y234 D238
• Enzyme Commision number: 3.1.13.-

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

External links

• PDB: RCSB:4oo1, PDBe:4oo1, PDBj:4oo1
• PDBsum: 4oo1
• PubMed: 25043052
• UniProt: Q12149|RRP6_YEAST Exosome complex exonuclease RRP6 (Gene Name=RRP6)