Solution Structure of Urm1 from Saccharomyces Cerevisiae

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.3 of the entry. See complete history


Solution structure of Urm1 and its implications for the origin of protein modifiers.

Xu, J.Zhang, J.Wang, L.Zhou, J.Huang, H.Wu, J.Zhong, Y.Shi, Y.

(2006) Proc Natl Acad Sci U S A 103: 11625-11630

  • DOI: https://doi.org/10.1073/pnas.0604876103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology, Hefei, Anhui 230026, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical 11.0 kDa protein in FAA3-MAS3 intergenic region107Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YIL008W
Find proteins for P40554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40554 
Go to UniProtKB:  P40554
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40554
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-09
    Changes: Data collection, Database references, Derived calculations