Structure of PDB 5c0w Chain J

Receptor sequence

>5c0wJ (length=970) Species: 559292 (Saccharomyces cerevisiae S288C)

RRKRLADGLSVTQKVFVRSRNGGATKIVREHYLRSDIPCLSRSCTKCPQI
VVPDAQNELPKFILSDSPLELSAPIGKHYVVLDTNVVLQAIDLLENPNCF
FDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDHKRFIVFHNEFSEHTFV
ERLPNETINDRNNRAIRKTCQWYSEHLKPYDINVVLVTNDRLNREAATKE
VESNIITKSLVQYIELLPNADDIRDSIPQMTFSDFTFPEYYSTARVMGGL
KNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQVIV
ELLPQSEWKAPSSIVLDSEHFDVNDNPDINTTVISDKQRRLLAKDAMIAQ
RSKKIQPTAKVVYIQRRSWRQYVGQLAPSSVDPQSSSTQNVFVILMDKCL
PKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAET
EALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTKR
KDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGT
ALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELD
DSANIVNVNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLS
VKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFM
LLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLE
SSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRH
YGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMIC
RNINRKHRNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVP
KFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEV
QVRSVMDPITSKRKAELLLK

3D structure

• PDB: 5c0w RNA degradation paths in a 12-subunit nuclear exosome complex.
• Chain: J
• Resolution: 4.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D543 D549 N551 D552 Y654 R847
• Catalytic site (residue number reindexed from 1): D512 D518 N520 D521 Y623 R816
• 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	J	N277 R397 D543 P544 C547 D549 N551 Y595 Y654 L696 E728 M731 L732 R753 H755 M813 M814 A815 A816 H831 L834 Y839 T843 R847 R889 R896	N259 R366 D512 P513 C516 D518 N520 Y564 Y623 L665 E697 M700 L701 R722 H724 M782 M783 A784 A785 H800 L803 Y808 T812 R816 R858 R865
BS02	MG	J	D543 D552	D512 D521
BS03	ZN	J	C47 C52 H184	C39 C44 H176

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:5c0w, PDBe:5c0w, PDBj:5c0w
• PDBsum: 5c0w
• PubMed: 26222026
• UniProt: Q08162|RRP44_YEAST Exosome complex exonuclease DIS3 (Gene Name=DIS3)