Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family

Abstract

The yabJ gene in Bacillus subtilis is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The molecular mechanism of YabJ is unknown. YabJ is a member of a large, widely distributed family of proteins of unknown biochemical function. The 1.7-Å crystal structure of YabJ reveals a trimeric organization with extensive buried hydrophobic surface and an internal water-filled cavity. The most important finding in the structure is a deep, narrow cleft between subunits lined with nine side chains that are invariant among the 25 most similar homologs. This conserved site is proposed to be a binding or catalytic site for a ligand or substrate that is common to YabJ and other members of the YER057c͞YjgF͞ UK114 family of proteins.

PurF-Independent Phosphoribosyl Amine Formation inyjgFMutants ofSalmonella entericaUtilizes the Tryptophan Biosynthetic Enzyme Complex Anthranilate Synthase-Phosphoribosyltransferase

“…Relevant to this study is the fact that the need for both PurF and the oxidative pentose phosphate pathway enzymes (e.g., Gnd) for PRA synthesis can be overcome by inactivating yjgF (14). Though YjgF is conserved throughout the three domains of life and has been the subject of numerous structural studies (2,7,8,22,23,31,42,46), its specific role in the cell is not known. This study was initiated to understand the cellular role of the YjgF protein in the context of thiamine synthesis by probing the mechanism used to generate PRA in a purF yjgF gnd mutant background.…”

“…The biochemical function of the YjgF protein, and all proteins in the YjgF/YER057c/UK114 family, remains unknown (21,41), although more than seven high-resolution structures of family members have been described (2,7,8,22,23,31,42,46).…”

Conserved YjgF Protein Family Deaminates Reactive Enamine/Imine Intermediates of Pyridoxal 5′-Phosphate (PLP)-dependent Enzyme Reactions

“…YjgF and IlvA proteins were present at monomeric concentrations of 1.6 and 0.9 M, respectively. Because YjgF is a trimer (1,2) and IlvA is a tetramer (28), the YjgF:IlvA oligomeric ratio in these experiments was ϳ2:1. Results from the spectrophotometric assay were corroborated by two independent methods that quantified 2-ketobutyrate using a discontinuous assay.…”

The σ B -Dependent yabJ-spoVG Operon Is Involved in the Regulation of Extracellular Nuclease, Lipase, and Protease Expression in Staphylococcus aureus

“…The molecular mechanisms of YabJ, which belongs to the YjgF protein family of unknown biochemical function (49), and of the stage V sporulation protein G SpoVG (30), originally identified in Bacillus subtilis as being involved in the formation of the spore cortex, are yet unknown for the nonsporulating S. aureus. However, the finding that inactivation of the staphylococcal yabJ-spoVG operon, like inactivation of B , reduces the transcription of the capA gene, which is not preceded by a B promoter (36), and reduces the resistance level of methicillin-resistant S. aureus (MRSA) and glycopeptide intermediate-resistant S. aureus (GISA) (46) support the hypothesis that the yabJ-spoVG operon may encode a B downstream regulatory element.…”