HMM Summary Page: TIGR03471

Functionhopanoid biosynthesis associated radical SAM protein HpnJ
Gene SymbolhpnJ
Trusted Cutoff577.60
Domain Trusted Cutoff577.60
Noise Cutoff577.40
Domain Noise Cutoff577.40
Isology Typehypoth_equivalog
HMM Length472
AuthorSelengut J
Entry DateAug 10 2007 9:21AM
Last ModifiedFeb 14 2011 3:27PM
CommentThe sequences represented by this model are members of the radical SAM superfamily of enzymes (PF04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions [1]. The member of this clade from Acidithiobacillus ferrooxidans ATCC 23270 (AFE_0975) is found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. Similarly, in Ralstonia eutropha JMP134 (Reut_B4901) this gene is adjacent to HpnAB, IspH and HpnH (TIGR03470), although SHC itself is elsewhere in the genome. Notably, this gene (here named HpnJ) and three others form a conserved set (HpnIJKL) which occur in a subset of all genomes containing the SHC enzyme. This relationship was discerned using the method of partial phylogenetic profiling [2]. This group includes Zymomonas mobilis, the organism where the initial hopanoid biosynthesis locus was described consisting of the genes HpnA-E and SHC (HpnF) [3]. Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and another radical SAM enzyme (ZMO0874), HpnH. Although discontinuous in Z. mobilis, we continue the gene symbol sequence with HpnIJKL. One of the well-described hopanoid intermediates is bacteriohopanetetrol. In the conversion from hopene several reactions must occur in the side chain for which a radical mechanism might be reasonable. These include the four (presumably anaerobic) hydroxylations and a methyl shift.
ReferencesRN [1] RM PMID:11222759 RT Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. RA Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE RL Nucleic Acids Res. 2001 Mar 1;29(5):1097-106. RN [2] RM PMID:16930487 RT Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. RA Haft DH, Paulsen IT, Ward N, Selengut JD RL BMC Biol. 2006 Aug 24;4:29. RN [3] RM PMID:9714766 RT Cloning of conserved genes from Zymomonas mobilis and Bradyrhizobium japonicum that function in the biosynthesis of hopanoid lipids. RA Perzl M, Reipen IG, Schmitz S, Poralla K, Sahm H, Sprenger GA, Kannenberg EL RL Biochim Biophys Acta. 1998 Jul 31;1393(1):108-18.
Genome PropertyGenProp0761: hopanoid lipid biosynthesis (HMM)