Crystal structure of yeast YER010Cp, a knotable member of the RraA protein family

Abstract

We present here the structure of Yer010c protein of unknown function, solved by Multiple Anomalous Diffraction and revealing a common fold and oligomerization state with proteins of the regulator of ribonuclease activity A (RraA) family. In Escherichia coli, RraA has been shown to regulate the activity of ribonuclease E by direct interaction. The absence of ribonuclease E in yeast suggests a different function for this family member in this organism. Yer010cp has a few supplementary secondary structure elements and a deep pseudo-knot at the heart of the protein core. A tunnel at the interface between two monomers, lined with conserved charged residues, has unassigned residual electron density and may constitute an active site for a yet unknown activity.

Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida

“…Interestingly, GalC shows a significant amino acid sequence identity with proteins of the RraA family, e.g. the Yer010c protein from Saccharomyces cerevisiae (Table 1) , that were originally misannotated as S ‐adenosylmethionine‐dependent methyltransferases but whose three‐dimensional structure resembles the phosphohistidine domains of phosphotransfer systems (Leulliot et al ., 2005). Based on the known three‐dimensional structure of the Yer010c protein (Leulliot et al ., 2005), the predicted structure of the GalC monomer fits a α−β−β−α sandwich (Fig.…”

“…the Yer010c protein from Saccharomyces cerevisiae (Table 1) , that were originally misannotated as S ‐adenosylmethionine‐dependent methyltransferases but whose three‐dimensional structure resembles the phosphohistidine domains of phosphotransfer systems (Leulliot et al ., 2005). Based on the known three‐dimensional structure of the Yer010c protein (Leulliot et al ., 2005), the predicted structure of the GalC monomer fits a α−β−β−α sandwich (Fig. S7B), being the last α5 and α6 helices likely involved in oligomerization of the protein and accounting for the hexameric quaternary conformation reported in native CHA aldolases from different bacteria (Tack et al ., 1972b; Maruyama, 1990; Hara et al ., 2003).…”

“…A multiple sequence alignment among GalC, other CHA aldolases and proteins of the RraA family reveals highly conserved residues, including R123 and D124 in GalC (Fig. S7C), that have been postulated to be involved in a phosphotransfer reaction (Leulliot et al ., 2005). Residues C95 and C159 in GalC are also conserved in other CHA aldolases (Fig.…”

Structural and Kinetic Characterization of 4-Hydroxy-4-methyl-2-oxoglutarate/4-Carboxy-4-hydroxy-2-oxoadipate Aldolase, a Protocatechuate Degradation Enzyme Evolutionarily Convergent with the HpaI and DmpG Pyruvate Aldolases

“…There are two relatively close structural homologs to HMG/CHA aldolase that are functionally uncharacterized: PSPTO_3204 (Protein Data Bank code 3K4I) from Pseudomonas syringae pv. tomato DC3000 and YER010c (Protein Data Bank code 2C5Q) from Saccharomyces cerevisiae (11 (Table 2). Using Mg 2ϩ or Mn 2ϩ as cofactors, the substrate specificity of HMG/CHA aldolase toward different 4-hydroxy-2-ketoacids was determined (Table 3).…”

“…Therefore, HMG/CHA aldolases have been proposed to be distinct members of Class II pyruvate aldolases in aromatic degradation pathways (COG0684 for HMG/CHA aldolases, COG3836 for HpaI, and COG0119 for DmpG). Intriguingly, the HMG/CHA aldolases are distantly related in sequence to RraA (regulator of ribonuclease activity A) proteins (sequence identities of 25-33% over the central ϳ115 residues and ϳ15% over entire sequence), which associate within the RNA degradosome and inhibit RNase E activity in Escherichia coli (10), and a yeast protein (YER010c) of known structure but unknown function (11).…”