PDBsum entry 2ax5

Signaling protein

PDB id: 2ax5

Contents

Protein chain

99 a.a. *

* Residue conservation analysis

PDB id:

2ax5

Name:

Signaling protein

Title:

Solution structure of urm1 from saccharomyces cerevisiae

Structure:

Hypothetical 11.0 kda protein in faa3-mas3 intergenic region. Chain: a. Synonym: ubiquitin-related modifier-1. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: yil008w. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

20 models

Authors:

J.Xu,H.Huang,J.Zhang,J.Wu,Y.Shi

Key ref:

J.Xu et al. (2006). Solution structure of Urm1 and its implications for the origin of protein modifiers. Proc Natl Acad Sci U S A, 103, 11625-11630. PubMed id: 16864801 DOI: 10.1073/pnas.0604876103

Date:

03-Sep-05 Release date: 27-Jun-06

Protein chain

P40554  (URM1_YEAST) -  Ubiquitin-related modifier 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 99 a.a.

Struc: 99 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.0604876103

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

PubMed id: 16864801

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

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

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.

Selected figure(s)

Figure 1.
NMR structure of Urm1. (A) Backbone overlay of 20 NMR structures with the lowest energy from the final CNS v.1.1 calculation. (B) Ribbon representation of Urm1 (strand β4* was identified by NOE connectivity).

Figure 3.
Structure–function relationship between Urm1 and MoaD (PDB code 1FMA chainD). (A and B) Solvent-exposed residues (yellow balls) and nearby electrostatic residues (sticks, Arg in blue and Asp in red) were superimposed on the ribbon representation of Urm1 (A) and MoaD (B). (C and D) Electrostatic surface diagrams of Urm1 (C) and MoaD (D). The surface color reflects the magnitude of the electrostatic potential: red, negative; blue, positive; white, neutral. All of the surfaces were observed from the same orientation.

Figures were selected by an automated process.