Structure of PDB 8k5p Chain M Binding Site BS01

Receptor Information
>8k5p Chain M (length=744) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPSFFRWLSRKYPKIISPVLEEQPQIVDGVILPLDYSASNPNGELDNLYL
DMNGIVHPCSHPENKPPPETEDEMLLAVFEYTNRVLNMARPRKVLVMAVD
GVAPRAKMNQQRARRFRSARDAQIENEAREEIMRQREEVGEIIDDAVRNK
KTWDSNAITPGTPFMDKLAAALRYWTAFKLATDPGWKNLQVIISDATVPG
EGEHKIMNFIRSQRADPEYNPNTTHCIYGLDADLIFLGLATHEPHFKILR
EDVFAQDNRKRNNLKDTINMTEEEKQFLQKQNSEQPFLWLHINVLREYLS
AELWVPGLPFTFDLERAIDDWVFMCFFCGNDFLPHLPCLDVRENSIDILL
DIWKVVLPKLKTYMTCDGVLNLPSVETLLQHLGSREGDIFKTRHIQEARK
KEVFDTDEFVKLFEPGYHERYYTAKFHVTPQDIEQLRKDMVKCYIEGVAW
VLMYYYQGCASWNWFYPYHYAPLATDFHGFSHLEIKFEEGTPFLPYEQLM
SVLPAASGHALPKIFRSLMSEPDSEIIDFYPEEFPIDMNGKKMSWQGIAL
LPFIDQDRLLTAVRAQYPLLSDAERARNIRGEPVLLISNKNANYERFSKK
LYSKENNNNNVVVKFQHFKSGLSGIVSKDVEGFELNGKIVCPIQGGSLPN
LSTTLILKMSYRLIPLPSRNKSIILNGFIPSEPVLTAYDLDSIMYKYNNQ
NYSRRWNFGNDLKQNIVPVGPKGITQYKPRTGGYRAFFYFAELS
Ligand information
>8k5p Chain P (length=20) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
acagauguccucgagaggua
....................
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8k5p Structural basis of exoribonuclease-mediated mRNA transcription termination
Resolution2.8 Å
Binding residue
(original residue number in PDB)		P4 R8 R12 H59 Q113 R116 R117 L232 D233 K729 M730 W732 Q733 Y889 R892 N894 F895
Binding residue
(residue number reindexed from 1)		P2 R6 R10 H57 Q111 R114 R115 L230 D231 K542 M543 W545 Q546 Y702 R705 N707 F708
Enzymatic activity
Enzyme Commision number 3.1.13.-
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0004527 exonuclease activity
GO:0004534 5'-3' RNA exonuclease activity
GO:0005515 protein binding
GO:0019843 rRNA binding
Biological Process
GO:0000398 mRNA splicing, via spliceosome
GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006353 DNA-templated transcription termination
GO:0006364 rRNA processing
GO:0006397 mRNA processing
GO:0030846 termination of RNA polymerase II transcription, poly(A)-coupled
GO:0030847 termination of RNA polymerase II transcription, exosome-dependent
GO:0034244 negative regulation of transcription elongation by RNA polymerase II
GO:0043144 sno(s)RNA processing
GO:0071028 nuclear mRNA surveillance
GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process
GO:0110155 NAD-cap decapping
GO:1904595 positive regulation of termination of RNA polymerase II transcription
Cellular Component
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0090730 Las1 complex
GO:0110103 RNA polymerase II termination complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8k5p, PDBe:8k5p, PDBj:8k5p
PDBsum8k5p
PubMed38538796
UniProtQ02792|XRN2_YEAST 5'-3' exoribonuclease 2 (Gene Name=RAT1)

[Back to BioLiP]