Modomics - A Database of RNA Modifications

ID Card:

Full name: Elongator complex protein 1
Synonym: IKI3, TOT1
GI: 2498477
Orf: L3502.7
COG: COG5290
UniProt: Q06706
Structures: | 5CQS | 6QK7 |
Alpha Fold Predicted Structure: AF-Q06706-F1
Complex: Elongator complex


PDB Structures:


5CQS

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The evolutionarily conserved Elongator complex, which is composed of six subunits elongator protein 1 (Elp1 to -6), plays vital roles in gene regulation. The molecular hallmark of familial dysautonomia (FD) is the splicing mutation of Elp1 [also known as IκB kinase complex-associated protein (IKAP)] in the nervous system that is believed to be the primary cause of the devastating symptoms of this disease. Here, we demonstrate that disease-related mutations in Elp1 affect Elongator assembly, and we have determined the structure of the C-terminal portion of human Elp1 (Elp1-CT), which is sufficient for full-length Elp1 dimerization, as well as the structure of the cognate dimerization domain of yeast Elp1 (yElp1-DD). Our study reveals that the formation of the Elp1 dimer contributes to its stability in vitro and in vivo and is required for the assembly of both the human and yeast Elongator complexes. Functional studies suggest that Elp1 dimerization is essential for yeast viability. Collectively, our results identify the evolutionarily conserved dimerization domain of Elp1 and suggest that the pathological mechanisms underlying the onset and progression of Elp1 mutation-related disease may result from impaired Elongator activities.

Download RCSB-PDB Structures:

Pdb Files   5CQS.pdb   6QK7.pdb  
Pdbx/mmCIF Files   5CQS.cif   6QK7.cif  


Protein sequence:

MVEHDKSGSKRQELRSNMRNLITLNKGKFKPTASTAEGDEDDLSFTLLDSVFDTLSDSITCVLGSTDIGAIEVQQFMKDGSRNVLASFNIQTFDDKLLSFVHFADINQLVFVFEQGDIITATYDPVSLDPAETLIEIMGTIDNGIAAAQWSYDEETLAMVTKDRNVVVLSKLFEPISEYHLEVDDLKISKHVTVGWGKKETQFRGKGARAMEREALASLKASGLVGNQLRDPTMPYMVDTGDVTALDSHEITISWRGDCDYFAVSSVEEVPDEDDETKSIKRRAFRVFSREGQLDSASEPVTGMEHQLSWKPQGSLIASIQRKTDLGEEDSVDVIFFERNGLRHGEFDTRLPLDEKVESVCWNSNSEALAVVLANRIQLWTSKNYHWYLKQELYASDISYVKWHPEKDFTLMFSDAGFINIVDFAYKMAQGPTLEPFDNGTSLVVDGRTVNITPLALANVPPPMYYRDFETPGNVLDVACSFSNEIYAAINKDVLIFAAVPSIEEMKKGKHPSIVCEFPKSEFTSEVDSLRQVAFINDSIVGVLLDTDNLSRIALLDIQDITQPTLITIVEVYDKIVLLRSDFDYNHLVYETRDGTVCQLDAEGQLMEITKFPQLVRDFRVKRVHNTSAEDDDNWSAESSELVAFGITNNGKLFANQVLLASAVTSLEITDSFLLFTTAQHNLQFVHLNSTDFKPLPLVEEGVEDERVRAIERGSILVSVIPSKSSVVLQATRGNLETIYPRIMVLAEVRKNIMAKRYKEAFIVCRTHRINLDILHDYAPELFIENLEVFINQIGRVDYLNLFISCLSEDDVTKTKYKETLYSGISKSFGMEPAPLTEMQIYMKKKMFDPKTSKVNKICDAVLNVLLSNPEYKKKYLQTIITAYASQNPQNLSAALKLISELENSEEKDSCVTYLCFLQDVNVVYKSALSLYDVSLALLVAQKSQMDPREYLPFLQELQDNEPLRRKFLIDDYLGNYEKALEHLSEIDKDGNVSEEVIDYVESHDLYKHGLALYRYDSEKQNVIYNIYAKHLSSNQMYTDAAVAYEMLGKLKEAMGAYQSAKRWREAMSIAVQKFPEEVESVAEELISSLTFEHRYVDAADIQLEYLDNVKEAVALYCKAYRYDIASLVAIKAKKDELLEEVVDPGLGEGFGIIAELLADCKGQINSQLRRLRELRAKKEENPYAFYGQETEQADDVSVAPSETSTQESFFTRYTGKTGGTAKTGASRRTAKNKRREERKRARGKKGTIYEEEYLVQSVGRLIERLNQTKPDAVRVVEGLCRRNMREQAHQIQKNFVEVLDLLKANVKEIYSISEKDRERVNENGEVYYIPEIPVPEIHDFPKSHIVDF

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

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-Q06706-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q06706-F1.cif  
DSSP Secondary Structures   Q06706.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 -
Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Otero G, Fellows J, Li Y, de Bizemont T, Dirac AM, Gustafsson CM, Erdjument-Bromage H, Tempst P, Svejstrup JQ... Mol Cell [details] 10024884 -