Taxonomic distribution of proteins containing YceI domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing YceI domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Crystal structure of a novel polyisoprenoid-binding protein from Thermusthermophilus HB8.

Handa N, Terada T, Doi-Katayama Y, Hirota H, Tame JR, Park SY, Kuramitsu S, Shirouzu M, Yokoyama S
Protein Sci. 2005; 14: 1004-10

The isoprenoid quinones exist widely among prokaryotes and eukaryotes.They play essential roles in respiratory electron transport and incontrolling oxidative stress and gene regulation. In the isoprenoidquinone biosynthetic pathway, polyprenyl pyrophosphates are used asisoprenoid side-chain precursors. Here we report the crystal structure ofa novel polyprenyl pyrophosphate binding protein, TT1927b, from Thermusthermophilus HB8, complexed with its ligand. This protein belongs to theYceI-like family in the Pfam database, and its sequence homologs arepresent in a broad range of bacteria and archaea. The structure consistsof an extended, eight-stranded, antiparallel beta-barrel. In thehydrophobic pore of the barrel, the protein binds the polyisoprenoid chainby hydrophobic interactions. Its overall structure resembles the lipocalinfold, but there is no sequence homology between TT1927b and the lipocalinfamily of proteins.

pH-dependent expression of periplasmic proteins and amino acid catabolismin Escherichia coli.

Stancik LM, Stancik DM, Schmidt B, Barnhart DM, Yoncheva YN, Slonczewski JL
J Bacteriol. 2002; 184: 4246-58

Escherichia coli grows over a wide range of pHs (pH 4.4 to 9.2), and itsown metabolism shifts the external pH toward either extreme, depending onavailable nutrients and electron acceptors. Responses to pH values acrossthe growth range were examined through two-dimensional electrophoresis(2-D gels) of the proteome and through lac gene fusions. Strain W3110 wasgrown to early log phase in complex broth buffered at pH 4.9, 6.0, 8.0, or9.1. 2-D gel analysis revealed the pH dependence of 19 proteins notpreviously known to be pH dependent. At low pH, several acetate-inducedproteins were elevated (LuxS, Tpx, and YfiD), whereas acetate-repressedproteins were lowered (Pta, TnaA, DksA, AroK, and MalE). These responsescould be mediated by the reuptake of acetate driven by changes in pH. Theamplified proton gradient could also be responsible for the acid inductionof the tricarboxylic acid (TCA) enzymes SucB and SucC. In addition to theautoinducer LuxS, low pH induced another potential autoinducer component,the LuxH homolog RibB. pH modulated the expression of several periplasmicand outer membrane proteins: acid induced YcdO and YdiY; base inducedOmpA, MalE, and YceI; and either acid or base induced OmpX relative to pH7. Two pH-dependent periplasmic proteins were redox modulators: Tpx(acid-induced) and DsbA (base-induced). The locus alx, induced in extremebase, was identified as ygjT, whose product is a putative membrane-boundredox modulator. The cytoplasmic superoxide stress protein SodB wasinduced by acid, possibly in response to increased iron solubility. HighpH induced amino acid metabolic enzymes (TnaA and CysK) as well as lacfusions to the genes encoding AstD and GabT. These enzymes participate inarginine and glutamate catabolic pathways that channel carbon into acidsinstead of producing alkaline amines. Overall, these data are consistentwith a model in which E. coli modulates multiple transporters and pathwaysof amino acid consumption so as to minimize the shift of its external pHtoward either acidic or alkaline extreme.