Modomics - A Database of RNA Modifications

ID Card:

Full name: NAD-capped RNA hydrolase NUDT12
GI: 68565930
UniProt: Q9BQG2
Structures: | 6SCX |
Alpha Fold Predicted Structure: AF-Q9BQG2-F1
Enzyme type: hydrolase


PDB Structures:


6SCX

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

RNA polymerase II transcripts receive a protective 5',5'-triphosphate-linked 7-methylguanosine (m 7 G) cap, and its removal by decapping enzymes like DCP2 is critical for initiation of RNA decay. Alternative RNA caps can be acquired when transcription initiation uses metabolites like nicotinamide adenine dinucleotide (NAD), generating NAD-RNAs. Here, we identify human NUDT12 as a cytosolic NAD-RNA decapping enzyme. NUDT12 is active only as homodimers, with each monomer contributing to creation of the two functional catalytic pockets. We identify an ∼600-kDa dodecamer complex between bleomycin hydrolase (BLMH) and NUDT12, with BLMH being required for localization of NUDT12 to a few discrete cytoplasmic granules that are distinct from P-bodies. Both proteins downregulate gene expression when artificially tethered to a reporter RNA in vivo. Furthermore, loss of Nudt12 results in a significant upregulation of circadian clock transcripts in mouse liver. Overall, our study points to a physiological role for NUDT12 in the cytosolic surveillance of NAD-RNAs.

Download RCSB-PDB Structures:

Pdb Files   6SCX.pdb  
Pdbx/mmCIF Files   6SCX.cif  


Protein sequence:

MSSVKRSLKQEIVTQFHCSAAEGDIAKLTGILSHSPSLLNETSENGWTALMYAARNGHPEIVQFLLEKGCDRSIVNKSRQTALDIAVFWGYKHIANLLATAKGGKKPWFLTNEVEECENYFSKTLLDRKSEKRNNSDWLLAKESHPATVFILFSDLNPLVTLGGNKESFQQPEVRLCQLNYTDIKDYLAQPEKITLIFLGVELEIKDKLLNYAGEVPREEEDGLVAWFALGIDPIAAEEFKQRHENCYFLHPPMPALLQLKEKEAGVVAQARSVLAWHSRYKFCPTCGNATKIEEGGYKRLCLKEDCPSLNGVHNTSYPRVDPVVIMQVIHPDGTKCLLGRQKRFPPGMFTCLAGFIEPGETIEDAVRREVEEESGVKVGHVQYVACQPWPMPSSLMIGCLALAVSTEIKVDKNEIEDARWFTREQVLDVLTKGKQQAFFVPPSRAIAHQLIKHWIRINPNL

Comments:

mRNA decapping enzyme that specifically removes the nicotinamide adenine dinucleotide (NAD) cap from a subset of mRNAs by hydrolyzing the diphosphate linkage to produce nicotinamide mononucleotide (NMN) and 5' monophosphate mRNA





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q9BQG2-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9BQG2-F1.cif  
DSSP Secondary Structures   Q9BQG2.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structural and mechanistic basis of mammalian Nudt12 RNA deNADding. Ewa Grudzien-Nogalska,Yixuan Wu,Xinfu Jiao,Huijuan Cui,Maria K Mateyak,Ronald P Hart,Liang Tong,Megerditch Kiledjian Nat Chem Biol [details] 31101919 -