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PDBsum entry 2ax5
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Signaling protein
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PDB id
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2ax5
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References listed in PDB file
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Key reference
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Title
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Solution structure of urm1 and its implications for the origin of protein modifiers.
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Authors
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J.Xu,
J.Zhang,
L.Wang,
J.Zhou,
H.Huang,
J.Wu,
Y.Zhong,
Y.Shi.
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Ref.
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Proc Natl Acad Sci U S A, 2006,
103,
11625-11630.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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).
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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.
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