The three far-upstream element (FUSE) binding protein (FBP) family members have been ascribed different functions in gene regulation. They were therefore examined with various biochemical, molecular biological, and cell biological tests to evaluate whether their sequence differences reflect functional customization or neutral changes at unselected residues. Each FBP displayed a characteristic profile of intrinsic transcription activation and repression, binding with protein partners, and subcellular trafficking. Although some differences, such as weakened FBP3 nuclear localization, were predictable from primary sequence differences, the unexpected failure of FBP3 to bind the FBP-interacting repressor (FIR) was traced to seemingly conservative substitutions within a small patch of an N-terminal ␣-helix. The transactivation strength and the FIR-binding strength of the FBPs were in the opposite order. Despite their distinguishing features and differential activities, the FBPs traffic to shared subnuclear sites and regulate many common target genes, including c-myc. Though a variety of functions have been attributed to the FBPs, based upon their panel of shared and unique features, we propose that they constitute a molecular regulatory kit that tunes the expression of shared targets through a common mechanism.The far-upstream element (FUSE) binding protein (FBP) binds the FUSE of the human c-myc proto-oncogene (1, 10, 16, 32). The DNA-binding domain (DBD) of FBP contains four repeated hnRNPK homology (KH) motifs. Though they are commonly called an RNA-binding motif, some KH domain proteins-including hnRNP K, the prototype of this familyengage single-stranded DNA with an affinity and sequence specificity equal to or greater than those of RNA (3,4,10,16,32). The carboxyl-terminal domain of FBP stimulates transcription complexes transiting between initiation and promoter escape via activation of the p89/XPB helicase subunit of TFIIH (29). Transcription activation requires at least one copy of a tyrosine-rich motif that is repeated three times in the carboxylterminal activation domain (AD) (11). The less well characterized amino terminus of FBP impairs the action of some, but not all, transcription activators (for example, FBP itself and E1a but not VP16) (11).FBP function is modified by at least two partner proteins. Recruited by FBP, the amino terminus of the FBP-interacting repressor (FIR) blunts AD-mediated stimulation of the p89/XPB helicase activity, permitting only basal transcription (27). Both FBP activation and FIR repression are blocked by mutations in p89/XPB. Associating with the AD, p38/JTV-1/AIMP2 targets FBP for ubiquitinylation and degradation (22). p38 was originally identified as a core protein of a multi-aminoacyl-tRNA synthetase complex (34,36,38,40), and the knockout of p38 in mice indeed dissociates this complex (21); nevertheless, the knockout pups, which develop to full term, support normal levels of protein synthesis (22). Hyperplasia of the lungs and some other organs cause neonatal lethality....