YgbB N terminal protein domain
In molecular biology, YgbB is a protein domain. This entry makes reference to a number of proteins from eukaryotes and prokaryotes which share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme thought to aid terpenoid and isoprenoid biosynthesis, a vital chemical in all living organisms. This protein domain is part of an enzyme which catalyses a reaction in a complex pathway.[1]
| YgbB | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 crystal structure of a 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase | |||||||||
| Identifiers | |||||||||
| Symbol | YgbB | ||||||||
| Pfam | PF02542 | ||||||||
| InterPro | IPR003526 | ||||||||
| SCOP2 | 1iv1 / SCOPe / SUPFAM | ||||||||
| CDD | cd0554 | ||||||||
| |||||||||
Function
The YgbB protein domain has a main function of being involved in terpenoid and isoprenoid biosynthesis.
Biochemistry
MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis.[2]
References
- Herz S, Wungsintaweekul J, Schuhr CA, Hecht S, Luttgen H, Sagner S, Fellermeier M, Eisenreich W, Zenk MH, Bacher A, Rohdich F (March 2000). "Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate to 2C-methyl-D-erythritol 2,4-cyclodiphosphate". Proc. Natl. Acad. Sci. U.S.A. 97 (6): 2486–90. doi:10.1073/pnas.040554697. PMC 15955. PMID 10694574.
- Kishida H, Wada T, Unzai S, Kuzuyama T, Takagi M, Terada T, Shirouzu M, Yokoyama S, Tame JR, Park SY (January 2003). "Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis". Acta Crystallogr. D. 59 (Pt 1): 23–31. doi:10.1107/s0907444902017705. PMID 12499535.