Structure of PDB 2hbl Chain A

Receptor sequence

>2hblA (length=390) Species: 4932 (Saccharomyces cerevisiae)

GMVEKPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDENNP
SHYPHPYEYEIDHQEYSPEILQIREEIPSKSWDDSVPIWVDTSTELESML
EDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHI
LNEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLPRH
SLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAAARADTHFLLNIYDQL
RNKLIESNKLAGVLYESRNVAKRRFEYSKYRPLTPSSEVYSPIEKESPWK
ILMYQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYT
PTDVIGVVSLTNGVTEHVRQNAKLLANLIRDALRNIKNTN

3D structure

• PDB: 2hbl Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain.
• Chain: A
• Resolution: 2.3 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D238 E240 D296 A361 D365
• Catalytic site (residue number reindexed from 1): D112 E114 D170 A235 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	ZN	A	E240 D365	E114 D239
BS02	MN	A	D238 D296	D112 D170
BS03	AMP	A	D238 E240 H241 W299 Q345	D112 E114 H115 W173 Q219

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:2hbl, PDBe:2hbl, PDBj:2hbl
• PDBsum: 2hbl
• PubMed: 16882719
• UniProt: Q12149|RRP6_YEAST Exosome complex exonuclease RRP6 (Gene Name=RRP6)