Clusters protein family

Likewise, for zinc, bacteria have developed active uptake systems (Hantke, 2001). In many bacteria the high-affinity Zn2+ uptake system uses an ABC transporter of the cluster 9 family, which mostly transports zinc and manganese and is found in nearly all bacterial species. First identified in cyanobacteria and pathogenic streptococci, but also found in E. coli, the system is encoded by three genes ZnuABC and consists of an outer membrane permease ZnuB, a periplasmic-binding protein ZnuA and a cytoplasmic ATPase ZnuC. Low-affinity transporters of the ZIP family, described later in this chapter, such as ZupT, have also been shown to be involved in bacterial zinc uptake. 

Finally, we propose that APR becomes phosphorylated by the putative APR-kinase April and thereby inactivated, as a second resistance mechanism in addition to the 16S rRNA methylation by KamB, during biosynthesis or thereafter. Because AprZ is significantly similar to the StrK protein, a member of the protein family of extracellular alkaline phosphates and a STR-phosphate-specific dephosphorylase (see Section 2.2.1.2), this modification is urgently suggested by presence of the conserved aprZ gene in the biosynthetic cluster. April is a member of the large kinase family comprising all the antibiotic and protein kinases. As in the STR producers, the postulated APR-phosphate would exported via the ABC transport system AprV/AprW and set free by dephosphorylation outside the cells via the phospatase AprZ. 

Ferran, E. A. Ferrara, P. (1992). Clustering proteins into families using artificial neural networks. Comput Appl Biosci 8,39-44. 

There are two different approaches to the protein sequence classification problem. One can use an unsupervised neural network to group proteins if there is no knowledge of the number and composition of final clusters (e.g., Ferran Ferrara, 1992). Or one can use supervised networks to classify sequences into known (existing) protein families (e.g., Wu et al., 1992). 

In addition to the mechanistic role in the nitrogenase enzymatic function, Fe-protein also participates at several stages in the biosynthesis of the nitrogenase proteins. Fe-protein is essential for the production of active MoFe-protein and is involved in both the synthesis of FeMo-cofactor and its insertion into cofactor-deficient MoFe-protein (40-42). Fe-protein may also function as an activator for the expression of alternative nitrogenases (43). In turn, formation of active Fe-protein requires the nifM gene product (44, 45), which perhaps functions either in cluster insertion or in promoting the correct subunit-subunit and subunit-cofactor interactions in the Fe-protein dimer (i.e., a chaperone-type role). The significant sequence conservation observed in the Fe-protein family may reflect the structural constraints associated with these diverse aspects of Fe-protein function. 

Akache, B. and Turcotte, B. (2002) New regulators of drug sensitivity in the family of yeast zinc cluster proteins. The Journal of Biological Chemistry, 277, 21254—21260. 

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