Modomics - A Database of RNA Modifications

ID Card:

Full name: Elongator complex protein 4
Synonym: HAP1, TOT7
GI: 6325155
COG: COG0467
UniProt: Q02884
Structures: | 4A8J | 4EJS |
Alpha Fold Predicted Structure: AF-Q02884-F1
Complex: Elongator complex


PDB Structures:


4A8J

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Elongator was initially described as an RNA polymerase II-associated factor but has since been associated with a broad range of cellular activities. It has also attracted clinical attention because of its role in certain neurodegenerative diseases. Here we describe the crystal structure of the Saccharomyces cerevisiae subcomplex of Elongator proteins 4, 5 and 6 (Elp456). The subunits each show almost identical RecA folds that form a heterohexameric ring-like structure resembling hexameric RecA-like ATPases. This structural finding is supported by different complementary in vitro and in vivo approaches, including the specific binding of the hexameric Elp456 subcomplex to tRNAs in a manner regulated by ATP. Our results support a role of Elongator in tRNA modification, explain the importance of each of the Elp4, Elp5 and Elp6 subunits for complex integrity and suggest a model for the overall architecture of the holo-Elongator complex.

Download RCSB-PDB Structures:

Pdb Files   4A8J.pdb   4EJS.pdb  
Pdbx/mmCIF Files   4A8J.cif   4EJS.cif  


Protein sequence:

MSFRKRGEILNDRGSGLRGPLLRGPPRTSSTPLRTGNRRAPGNVPLSDTTARLKKLNIADESKTKMGLDSSHVGVRPSPATSQPTTSTGSADLDSILGHMGLPLGNSVLVEEQSTTEFHSILGKLFAAQGIVHNRISDSSADKTRNGDTHVIVLSLNQMFAKELPGIYKGSRKQMKKNLISEEESKVTVQNLNETQRSTPSRYKDLKIAWKYKLADEKRLGSPDRDDIQQNSEYKDYNHQFDITTRLMPAPIASELTFIAPTQPVSTILSQIEQTIKRNDKKLIRIVIPSLLHPAMYPPKMFESSEIIGLMHGVRSLVKKYYERVVLFASISIDIITPPLLVLLRNMFDSVINLEPFNQEMTEFLERVYKSQPGKIQHGLVHILKLPVFTDRGEMRVLKSEWAFKNGRKKFEIEQWGIPVDDAEGSAASEQSHSHSHSDEISHNIPAKKTKISLDY

Comments:

One of the six protein cofactors required for the synthesis of 5-carboxymethyl group (cm5) on the wobble uridine-34 of a few tRNA. Acetate or acetyl-CoA is the donor of acetyl group, but the detailed mechanism of the reaction is still unknown. The cm5U derivative is the intermediate for further biochemical transformation of U34 derivative to either 5-methoxycarbonylmethyl uridine (mcm5U) catalysed by Trm9/Trm112 or 5-carbamoylmethyluridine (ncm5U) catalysed by a still unknown enzyme. Mutation in Elp (especially Elp3) influences telomeric gene silencing and DNA damage response. The multi-subunit complex El1-6 also interacts with elongating RNA polymerase II (RNAPII) is thought to facilitate transcription through histone acetylation.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q02884-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q02884-F1.cif  
DSSP Secondary Structures   Q02884.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. Huang B, Lu J, Bystrom AS RNA [details] 18755837 -
An early step in wobble uridine tRNA modification requires the Elongator complex. Huang B, Johansson MJ, Bystrom AS RNA [details] 15769872 -
Elongator complex influences telomeric gene silencing and DNA damage response by its role in wobble uridine tRNA modification. Chen C, Huang B, Eliasson M, Ryden P, Bystrom AS... PLoS Genet [details] 21912530 -