Structure of PDB 4ifd Chain J

Receptor sequence

>4ifdJ (length=948) Species: 559292 (Saccharomyces cerevisiae S288C)

RRKRLADGLSVTQKVFVRSRNGGATKIVREHYLRSDIPCLSRSCTKCPQI
VVPDAQNELPKFILSDSPLELSAPIGKHYVVLDTNVVLQAIDLLENPNCF
FDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDHKRFIVFHNEFSEHTFV
ERLPNETINDRNNRAIRKTCQWYSEHLKPYDINVVLVTNDRLNREAATKE
VESNIITKSLVQYIELLPNADDIRDSIPQTFSDFTFPEYYSTARVMGGLK
NGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQVIVE
LLPQSEWKAPVISDKQRRLLAKDAMIAQRSKKIQPTAKVVYIQRRSWRQY
VGQLAPSSVDPQSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISI
DSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECL
PAEGHDWKAPTKLDDPEAVSKDPLLTKRKDLRDKLICSIDPPGCVDINDA
LHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDM
LPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFS
YEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKV
HMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLR
RHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNT
LVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVV
AHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQFAGRASIEYYV
GQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAF
DEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK

3D structure

• PDB: 4ifd Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.
• Chain: J
• Resolution: 2.805 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D543 D549 N551 D552 Y654 R847
• Catalytic site (residue number reindexed from 1): D490 D496 N498 D499 Y601 R794
• 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 Q315 D543 P544 C547 D549 I550 N551 D552 Y595 Y654 L696 V727 E728 M731 L732 R753 H755 T810 M813 A815 A816 H831 Y839 H841 T843 R847 R882 R889 R896	N258 Q296 D490 P491 C494 D496 I497 N498 D499 Y542 Y601 L643 V674 E675 M678 L679 R700 H702 T757 M760 A762 A763 H778 Y786 H788 T790 R794 R829 R836 R843
BS02	MG	J	D543 D552	D490 D499
BS03	ZN	J	C47 C52 C55 H184	C39 C44 C47 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:4ifd, PDBe:4ifd, PDBj:4ifd
• PDBsum: 4ifd
• PubMed: 23376952
• UniProt: Q08162|RRP44_YEAST Exosome complex exonuclease DIS3 (Gene Name=DIS3)