Structure of PDB 5vzj Chain K

Receptor sequence

>5vzjK (length=956) Species: 559292 (Saccharomyces cerevisiae S288C)

PRRKRLADGLSVTQKVFVRSRNGGATKIVREHYLRSDIPCLSRSCTKCPQ
IVVPDAQNELPKFILSDSPLELSAPIGKHYVVLDTNVVLQAIDLLENPNC
FFDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDHKRFIVFHNEFSEHTF
VERLPNETINDRNNRAIRKTCQWYSEHLKPYDINVVLVTNDRLNREAATK
EVESNIITKSLVQYIELLPNADDIRDSIPQMDFTFPEYYSTARVMGGLKN
GVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQVIVEL
LPQSEWKAPSSIVLDSEHFDVNDNPDIEAVISDKQRRLLAKDAMIAQRSK
KIQPTAKVVYIQRRSWRQYVGQLAPSSVDPQSSSTQNVFVILMDKCLPKV
RIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAETEAL
LLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTKRKDL
RDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALD
AEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSA
NIVNVNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKL
KQKRLEAGALNLASPEVKVHMDDPNEVEIKKLLATNSLVEEFMLLANISV
ARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALAD
SLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDI
YTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKH
RNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGL
IRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMD
AELLLK

3D structure

• PDB: 5vzj Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase.
• Chain: K
• Resolution: 3.3 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D543 D549 N551 D552 Y654 R847
• Catalytic site (residue number reindexed from 1): D509 D515 N517 D518 Y620 R809
• Enzyme Commision number: 3.1.13.-
  3.1.26.-

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	K	D543 P544 D549 I550 N551 D552 Y595 Y654 E728 M731 L732 R753 H755 T810 R811 M813 M814 A815 A816 H831 L834 Y839 H841 T843 R847 R889 R896	D509 P510 D515 I516 N517 D518 Y561 Y620 E690 M693 L694 R715 H717 T772 R773 M775 M776 A777 A778 H793 L796 Y801 H803 T805 R809 R851 R858
BS02	ZN	K	C47 C52 C55 H184	C40 C45 C48 H177

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0000175 3'-5'-RNA exonuclease activity
• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0004519 endonuclease activity
• GO:0004521 RNA endonuclease activity
• GO:0004527 exonuclease activity
• GO:0004540 RNA nuclease activity
• GO:0005515 protein binding

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:0006364 rRNA processing
• GO:0006396 RNA processing
• GO:0006397 mRNA processing
• GO:0006401 RNA catabolic process
• GO:0016075 rRNA catabolic process
• GO:0043628 regulatory ncRNA 3'-end processing
• GO:0070651 nonfunctional rRNA decay
• GO:0071028 nuclear mRNA surveillance
• GO:0071031 nuclear mRNA surveillance of mRNA 3'-end processing
• GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process
• GO:0071038 TRAMP-dependent tRNA surveillance pathway
• GO:0071039 nuclear polyadenylation-dependent CUT catabolic process

Cellular Component

• GO:0000176 nuclear exosome (RNase complex)
• GO:0000177 cytoplasmic exosome (RNase complex)
• GO:0000178 exosome (RNase complex)
• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion

External links

• PDB: RCSB:5vzj, PDBe:5vzj, PDBj:5vzj
• PDBsum: 5vzj
• PubMed: 28742025
• UniProt: Q08162|RRP44_YEAST Exosome complex exonuclease DIS3 (Gene Name=DIS3)