Modomics - A Database of RNA Modifications

ID Card:

Full name: RNA decapping complex subunit 2
GI: 74675930
Orf: dcp2
COG: COG0494
UniProt: O13828
Structures: | 2A6T | 2QKL | 2QKM | 4A54 | 5J3T | 5J3Y | 5KQI | 5KQ4 | 5N2V |
Alpha Fold Predicted Structure: AF-O13828-F1
Enzyme type: hydrolase


PDB Structures:


2A6T

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Removal of the 5' cap on mRNA by the decapping enzyme Dcp2 is a critical step in 5'-to-3' mRNA decay. Understanding the structural basis of Dcp2 activity has been a challenge because Dcp2 is dynamic and has weak affinity for the cap substrate. Here we present a 2.6-Å-resolution crystal structure of a heterotrimer of fission yeast Dcp2, its essential activator Dcp1, and the human NMD cofactor PNRC2, in complex with a tight-binding cap analog. Cap binding is accompanied by a conformational change in Dcp2, thereby forming a composite nucleotide-binding site comprising conserved residues in the catalytic and regulatory domains. Kinetic analysis of PNRC2 revealed that a conserved short linear motif enhances both substrate affinity and the catalytic step of decapping. These findings explain why Dcp2 requires a conformational change for efficient catalysis and reveals that coactivators promote RNA binding and the catalytic step of decapping, possibly through different conformational states.

Download RCSB-PDB Structures:

Pdb Files   5KQ1.pdb   5KQ4.pdb   5N2V.pdb   5NFK.pdb  
Pdbx/mmCIF Files   5KQ1.cif   5KQ4.cif   5N2V.cif   5NFK.cif  


Protein sequence:

MSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTFKKNKPQTMKNKFYMVIPFLAPLKKWIKKRNIANNTTKEKNISVDVDADASSQLLSLLKSSTAPSDLATPQPSTFPQPPVESHSSFDIKQKILHLLNEGNEPKSPIQLPPVSNLPLNPPIQSSNSRLSHDNNSFDPFAYLGLDPKNPSASFPRVVSQNNMLTNKPVLNNHFQQSMYSNLLKDQNSVQHLFAASDMPSPMELPSPSTVYHQVFYPPTSTSVSSYGLGKTPQPAYGSSSPYVNGHQTQQISSLPPFQSQTQFLARNSDNSGQSYNSEGDSNSKRLLSMLSQQDTTPSSSTLSKEANVQLANLFLTPNSLETKKFSDNSQGEEISDNLHGESCNNPNANSVHSAQLLQALLHPSATETKEETPKKTSDSLSLLTLLKSGLPTPANDLQNKSQNNERKASSQVKELEVKNYSKSTDLLKKTLRIPRNDEPLEAANQFDLLKVSPQQKSEVPPKRNELSQSKLKNRKKKENSETNKNHVDMSPGFVKILKRSPLADQKKEDTQESDFKGSDDHFLSYLQSVVSSNSNGLH

Comments:

The Dcp2 protein removes the cap structure of mRNA by cleaving capped mRNA which allows initiating 5′ to 3′ degradation. Decapping holoenzyme is composed of the catalytic Dcp2 subunit and the coactivator Dcp1. Dcp1 and the substrate RNA promote the closed form of the enzyme and the catalytic step of decapping is rate limiting and accelerated by Dcp1.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-O13828-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-O13828-F1.cif  
DSSP Secondary Structures   O13828.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Decapping reaction of mRNA requires Dcp1 in fission yeast: its characterization in different species from yeast to human. Sakuno T, Araki Y, Ohya Y, Kofuji S, Takahashi S, Hoshino S, Katada T... J Biochem [details] 15671491 -

Links:

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