Modomics - A Database of RNA Modifications

ID Card:

Full name: Small RNA 2′-O-methyltransferase
Synonym: CORYMBOSA 2, HUA ENHANCER 1
GI: 15638615
Orf: T13K14.70
COG: COG2227
UniProt: Q9C5Q8
Structures: | 3HTX |
Alpha Fold Predicted Structure: AF-Q9C5Q8-F1
Enzyme type: methyltransferase
Position of modification - modification: miRNA: 3'end Nm


PDB Structures:


3HTX

Structure Description:

Title: Crystal structure of small RNA methyltransferase HEN1
Classification: TRANSFERASE/RNA
Technique: X-Ray Diffraction
Resolution: 3.1
R value free: 0.288
R value observed: 0.26
R value work: 0.26

Abstract of the PDB Structure's related Publication:

RNA silencing is a conserved regulatory mechanism in fungi, plants and animals that regulates gene expression and defence against viruses and transgenes. Small silencing RNAs of approximately 20-30 nucleotides and their associated effector proteins, the Argonaute family proteins, are the central components in RNA silencing. A subset of small RNAs, such as microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs in animals and siRNAs in Drosophila, requires an additional crucial step for their maturation; that is, 2'-O-methylation on the 3' terminal nucleotide. A conserved S-adenosyl-l-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologues are responsible for this specific modification. Here we report the 3.1 A crystal structure of full-length HEN1 from Arabidopsis in complex with a 22-nucleotide small RNA duplex and cofactor product S-adenosyl-l-homocysteine. Highly cooperative recognition of the small RNA substrate by multiple RNA binding domains and the methyltransferase domain in HEN1 measures the length of the RNA duplex and determines the substrate specificity. Metal ion coordination by both 2' and 3' hydroxyls on the 3'-terminal nucleotide and four invariant residues in the active site of the methyltransferase domain suggests a novel Mg(2+)-dependent 2'-O-methylation mechanism.

Download RCSB-PDB Structures:

Pdb Files   3HTX.pdb  
Pdbx/mmCIF Files   3HTX.cif  


Protein sequence:

MAGGGKHTPTPKAIIHQKFGAKASYTVEEVHDSSQSGCPGLAIPQKGPCLYRCHLQLPEFSVVSNVFKKKKDSEQSAAELALDKLGIRPQNDDLTVDEARDEIVGRIKYIFSDEFLSAEHPLGAHLRAALRRDGERCGSVPVSVIATVDAKINSRCKIINPSVESDPFLAISYVMKAAAKLADYIVASPHGLRRKNAYPSEIVEALATHVSDSLHSREVAAVYIPCIDEEVVELDTLYISSNRHYLDSIAERLGLKDGNQVMISRMFGKASCGSECRLYSEIPKKYLDNSSDASGTSNEDSSHIVKSRNARASYICGQDIHGDAILASVGYRWKSDDLDYDDVTVNSFYRICCGMSPNGIYKISRQAVIAAQLPFAFTTKSNWRGPLPREILGLFCHQHRLAEPILSSSTAPVKSLSDIFRSHKKLKVSGVDDANENLSRQKEDTPGLGHGFRCEVKIFTKSQDLVLECSPRKFYEKENDAIQNASLKALLWFSKFFADLDVDGEQSCDTDDDQDTKSSSPNVFAAPPILQKEHSSESKNTNVLSAEKRVQSITNGSVVSICYSLSLAVDPEYSSDGESPREDNESNEEMESEYSANCESSVELIESNEEIEFEVGTGSMNPHIESEVTQMTVGEYASFRMTPPDAAEALILAVGSDTVRIRSLLSERPCLNYNILLLGVKGPSEERMEAAFFKPPLSKQRVEYALKHIRESSASTLVDFGCGSGSLLDSLLDYPTSLQTIIGVDISPKGLARAAKMLHVKLNKEACNVKSATLYDGSILEFDSRLHDVDIGTCLEVIEHMEEDQACEFGEKVLSLFHPKLLIVSTPNYEFNTILQRSTPETQEENNSEPQLPKFRNHDHKFEWTREQFNQWASKLGKRHNYSVEFSGVGGSGEVEPGFASQIAIFRREASSVENVAESSMQPYKVIWEWKKEDVEKKKTDL

Comments:

HEN1 deposits the methyl group on to the 2' OH of the 3' terminal nucleotide in double stranded small RNAs. It is a step in miRNA and siRNA metabolism. The modification prevents the 3' uridylation and degradation of the RNA molecule. AdoMet is a methyl group donor. Animal homologue of Hen1 modifies piRNA and is important for germ cell development.





Alpha Fold Predicted Structure:




Downloading... [167674/837294]


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Protein sequence:

M A G G G K H T P T P K A I I H Q K F G A K A S Y T V E E V H D S S Q S G C P G L A I P Q K G P C L Y R C H L Q L P E F S V V S N V F K K K K D S E Q S A A E L A L D K L G I R P Q N D D L T V D E A R D E I V G R I K Y I F S D E F L S A E H P L G A H L R A A L R R D G E R C G S V P V S V I A T V D A K I N S R C K I I N P S V E S D P F L A I S Y V M K A A A K L A D Y I V A S P H G L R R K N A Y P S E I V E A L A T H V S D S L H S R E V A A V Y I P C I D E E V V E L D T L Y I S S N R H Y L D S I A E R L G L K D G N Q V M I S R M F G K A S C G S E C R L Y S E I P K K Y L D N S S D A S G T S N E D S S H I V K S R N A R A S Y I C G Q D I H G D A I L A S V G Y R W K S D D L D Y D D V T V N S F Y R I C C G M S P N G I Y K I S R Q A V I A A Q L P F A F T T K S N W R G P L P R E I L G L F C H Q H R L A E P I L S S S T A P V K S L S D I F R S H K K L K V S G V D D A N E N L S R Q K E D T P G L G H G F R C E V K I F T K S Q D L V L E C S P R K F Y E K E N D A I Q N A S L K A L L W F S K F F A D L D V D G E Q S C D T D D D Q D T K S S S P N V F A A P P I L Q K E H S S E S K N T N V L S A E K R V Q S I T N G S V V S I C Y S L S L A V D P E Y S S D G E S P R E D N E S N E E M E S E Y S A N C E S S V E L I E S N E E I E F E V G T G S M N P H I E S E V T Q M T V G E Y A S F R M T P P D A A E A L I L A V G S D T V R I R S L L S E R P C L N Y N I L L L G V K G P S E E R M E A A F F K P P L S K Q R V E Y A L K H I R E S S A S T L V D F G C G S G S L L D S L L D Y P T S L Q T I I G V D I S P K G L A R A A K M L H V K L N K E A C N V K S A T L Y D G S I L E F D S R L H D V D I G T C L E V I E H M E E D Q A C E F G E K V L S L F H P K L L I V S T P N Y E F N T I L Q R S T P E T Q E E N N S E P Q L P K F R N H D H K F E W T R E Q F N Q W A S K L G K R H N Y S V E F S G V G G S G E V E P G F A S Q I A I F R R E A S S V E N V A E S S M Q P Y K V I W E W K K E D V E K K K T D L
100200300400500600700800900SequenceGHITBSN

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-Q9C5Q8-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9C5Q8-F1.cif  
DSSP Secondary Structures   Q9C5Q8.dssp  





Publications:

Links:

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