Structure of PDB 5yjj Chain F

Receptor sequence
>5yjjF (length=442) Species: 176280 (Staphylococcus epidermidis ATCC 12228) [Search protein sequence]
KKVFKTEWAGRSLTIETGQLAKQANGAVLVRYGDTVVLSTATASKEPRFF
PLTVNYEEKMYAADEATLTARLIDRPIRPLFPKGYRHDVQIMNIVLSADP
DCSPEMAAMIGSSMALSVSDIPFQGPIAGVNVGYIDGKYVINPSVADKEI
SRLDLEVAGHKDAVNMVEAGASEITESEMLEAIFFGHEEIKRLVAFQQEI
IDHIQPIKQVYAILNDLIKEEVRRLIADEKIRPDGRKVDEIRPLESEVGL
LPRAHGSGLFTRGQTQALSVLTLGARFMHHYNFPNFSVGETGPVRAPGRR
EIGHGALGERALRYIIPDTQDFPYTIRIVSEVLESNGSSSQASICGSTLA
LMDAGVPIKAPVAGIAMGLVTRDDSYTILTDIQGMEDALGDMDFKVAGTK
DGITAIQMDIKIDGLTREVIEEALEQARQGRLAIMDHMLHTI
3D structure
PDB5yjj Characterization of Staphylococcus epidermidis Polynucleotide phosphorylase and its interactions with ribonucleases RNase J1 and RNase J2.
ChainF
Resolution2.2 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Enzyme Commision number 2.7.7.8: polyribonucleotide nucleotidyltransferase.
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 PO4 F R403 H407 S441 S442 S443 K498 R300 H304 S338 S339 S340 K395
BS02 MG F S441 D496 S338 D393
Gene Ontology
Molecular Function
GO:0000175 3'-5'-RNA exonuclease activity
GO:0000287 magnesium ion binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004654 polyribonucleotide nucleotidyltransferase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006396 RNA processing
GO:0006401 RNA catabolic process
GO:0006402 mRNA catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5yjj, PDBe:5yjj, PDBj:5yjj
PDBsum5yjj
PubMed29242153
UniProtQ8CST1|PNP_STAES Polyribonucleotide nucleotidyltransferase (Gene Name=pnp)

[Back to BioLiP]