Modomics - A Database of RNA Modifications

ID Card:

Full name: Ubiquitin-related modifier 1
GI: 45270480
COG: COG5131
UniProt: P40554
Structures: | 2AX5 | 2PKO | 2QJL |
Alpha Fold Predicted Structure: AF-P40554-F1
Enzyme type: thiosulfate sulfurtransferase


PDB Structures:


2AX5

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Protein modifiers are involved in diverse biological processes and regulate the activity or function of target proteins by covalently conjugating to them. Although ubiquitin and a number of ubiquitin-like protein modifiers (Ubls) in eukaryotes have been identified, no protein modifier has been found in prokaryotes; thus, their evolutionary origin remains a puzzle. To infer the evolutionary relationships between the protein modifiers and sulfur carrier proteins, we solved the solution NMR structure of the Urm1 (ubiquitin-related modifier-1) protein from Saccharomyces cerevisiae. Both structural comparison and phylogenetic analysis of the ubiquitin superfamily, with emphasis on the Urm1 family, indicate that Urm1 is the unique "molecular fossil" that has the most conserved structural and sequence features of the common ancestor of the entire superfamily. The similarities of 3D structure and hydrophobic and electrostatic surface features between Urm1 and MoaD (molybdopterin synthase small subunit) suggest that they may interact with partners in a similar manner, and similarities between Urm1-Uba4 and MoaD-MoeB establish an evolutionary link between ATP-dependent protein conjugation in eukaryotes and ATP-dependent cofactor sulfuration.

Download RCSB-PDB Structures:

Pdb Files   2AX5.pdb   2BH2.pdb   2PKO.pdb   2QJL.pdb  
Pdbx/mmCIF Files   2AX5.cif   2BH2.cif   2PKO.cif   2QJL.cif  


Protein sequence:

MVNVKVEFLGGLDAIFGKQRVHKIKMDKEDPVTVGDLIDHIVSTMINNPNDVSIFIEDDSIRPGIITLINDTDWELEGEKDYILEDGDIISFTSTLHGG

Comments:

Part of eukaryotic sulfur-relay system required for in 2-thiolation of mcm5S2U at tRNA wobble positions.





Alpha Fold Predicted Structure:






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Protein sequence:

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

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-P40554-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P40554-F1.cif  
DSSP Secondary Structures   P40554.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Leidel S, Pedrioli PG, Bucher T, Brost R, Costanzo M, Schmidt A, Aebersold R, Boone C, Hofmann K, Peter M Nature [details] 19145231 -
Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions. Noma A, Sakaguchi Y, Suzuki T Nucleic Acids Res [details] 19151091 -
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 -
Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems. Nakai Y, Nakai M, Hayashi H J Biol Chem [details] 18664566 -