Structure of PDB 5k36 Chain J Binding Site BS01

Receptor Information

>5k36 Chain J (length=467) Species: 559292 (Saccharomyces cerevisiae S288C)

MVEKPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDNPSHY
PHPYEYEIDHQEYSPEILQIREEIPSKSWDDSVPIWVDTSTELESMLEDL
KNTKEIAVNLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHILNE
VFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLPRHSLA
YLLENFANFKTSKKYQLADWRIRPLSKPMTAYARADTHFLLNIYDQLRNK
LIESNKLAGVLYESRNVAKRRFEYSKYRPLTPSSEVYSPIEKESPWKILM
YQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTPTD
VIGVVSLTNGVTEHVRQNAKLLANLIRDALRNIKNTNADGILLETISVPQ
IRDVMERFSVLCNSNTNSSILLGKILPREEHDIAYSKDGLPNKVKTEDIR
IRAQNFKSALANLEDII

Ligand information

>5k36 Chain L (length=17)

uauuauuuauuuuaaaa

.................

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5k36 Nuclear RNA Exosome at 3.1 angstrom Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): E240 H241 H291 G292 F294 W299 Y315 K319 R325 H326 S327 L328 Q345 W349
• Binding residue (residue number reindexed from 1): E111 H112 H162 G163 F165 W170 Y186 K190 R196 H197 S198 L199 Q216 W220

Enzymatic activity

• Catalytic site (original residue number in PDB): N238 E240 D296 Y361 D365
• Catalytic site (residue number reindexed from 1): N109 E111 D167 Y232 D236
• 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:5k36, PDBe:5k36, PDBj:5k36
• PDBsum: 5k36
• PubMed: 27818140
• UniProt: Q12149|RRP6_YEAST Exosome complex exonuclease RRP6 (Gene Name=RRP6)