Modomics - A Database of RNA Modifications

ID Card:

Full name: Scavenger mRNA-decapping enzyme DcpS
Synonym: DCS-1, Hint-related 7meGMP-directed hydrolase, HINT5
GI: 116241325
Orf: HSPC015
COG: COG5075
UniProt: Q96C86
Structures: | 1ST0 | 1ST4 | 1XML | 1XMM | 3BL7 | 3BL9 | 3BLA | 4QDE | 4QDV | 4QEB | 5OSY |
Alpha Fold Predicted Structure: AF-Q96C86-F1
Enzyme type: hydrolase


PDB Structures:


1ST0

Structure Description:

Title: Structure of DcpS bound to m7GpppG
Classification: RNA BINDING PROTEIN
Technique: X-Ray Diffraction
Resolution: 1.9
R value free: 0.231
R value observed:
R value work: 0.187

Abstract of the PDB Structure's related Publication:

Complete removal of residual N-7 guanine cap from degraded messenger RNA is necessary to prevent accumulation of intermediates that might interfere with RNA processing, export, and translation. The human scavenger decapping enzyme, DcpS, catalyzes residual cap hydrolysis following mRNA degradation, releasing N-7 methyl guanosine monophosphate and 5'-diphosphate terminated cap or mRNA products. DcpS structures bound to m(7)GpppG or m(7)GpppA reveal an asymmetric DcpS dimer that simultaneously creates an open nonproductive DcpS-cap complex and a closed productive DcpS-cap complex that alternate via 30 A domain movements. Structural and biochemical analysis suggests an autoregulatory mechanism whereby premature decapping mRNA is prevented by blocking the conformational changes that are required to form a closed productive active site capable of cap hydrolysis.

Download RCSB-PDB Structures:

Pdb Files   1ST0.pdb   1ST4.pdb   1XML.pdb   1XMM.pdb   3BL7.pdb   3BL9.pdb   3BLA.pdb   4QDE.pdb   4QDV.pdb   4QEB.pdb  
Pdbx/mmCIF Files   1ST0.cif   1ST4.cif   1XML.cif   1XMM.cif   3BL7.cif   3BL9.cif   3BLA.cif   4QDE.cif   4QDV.cif   4QEB.cif  


Protein sequence:

MADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS

Comments:

DCPS is a decapping scavenger enzyme that hydrolyzes residual cap structure following the 3’-to-5’ exosome-mediated mRNA decay pathway. Moreover, it catalyzes the cleavage of cap analog structures like 7-methylguanosine nucleoside triphosphate in 10 small capped oligoribonucleotides, releasing 5’-phosphorylated RNA fragments and 7-methylguanosine monophosphate (m7GMP). Methylations appear to have controversial roles in DCPS's cleaving efficiency where caps like tri-methyl guanosine nucleoside triphosphate (m3(2,2,7)GpppG) are cleaved with very poor efficiency and unmethylated cap analog (GpppG) witnesses no decapping activity, on mRNA molecules longer than 25 nucleotides. It does not hydrolyze 7-methylguanosine diphosphate (m7GDP) to m7GMP.





Alpha Fold Predicted Structure:




Parsing response... [317548/317548]


Clear Selection and Reset Camera

Protein sequence:

M A D A A P Q L G K R K R E L D V E E A H A A S T E E K E A G V G N G T C A P V R L P F S G F R L Q K V L R E S A R D K I I F L H G K V N E A S G D G D G E D A V V I L E K T P F Q V E Q V A Q L L T G S P E L Q L Q F S N D I Y S T Y H L F P P R Q L N D V K T T V V Y P A T E K H L Q K Y L R Q D L R L I R E T G D D Y R N I T L P H L E S Q S L S I Q W V Y N I L D K K A E A D R I V F E N P D P S D G F V L I P D L K W N Q Q Q L D D L Y L I A I C H R R G I R S L R D L T P E H L P L L R N I L H Q G Q E A I L Q R Y R M K G D H L R V Y L H Y L P S Y Y H L H V H F T A L G F E A P G S G V E R A H L L A E V I E N L E C D P R H Y Q Q R T L T F A L R A D D P L L K L L Q E A Q Q S
50100150200250300SequenceGHITSN

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-Q96C86-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q96C86-F1.cif  
DSSP Secondary Structures   Q96C86.dssp  





Publications:

Links:

_PubMed_