HMM Summary Page: TIGR03470

Functionhopanoid biosynthesis associated radical SAM protein HpnH
Gene SymbolhpnH
Trusted Cutoff225.05
Domain Trusted Cutoff225.05
Noise Cutoff162.35
Domain Noise Cutoff162.35
Isology Typehypoth_equivalog
HMM Length318
AuthorSelengut J
Entry DateAug 9 2007 3:38PM
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 members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF) [1]. Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH and running in the same convergent direction is IspH (ZM0875, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase), an essential enzyme of IPP biosynthesis and therefore essential for the biosynthesis of hopanoids. 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: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)