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
SymbolYgbB
PfamPF02542
InterProIPR003526
SCOP21iv1 / SCOPe / SUPFAM
CDDcd0554
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

Function

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The YgbB protein domain has a main function of being involved in terpenoid and isoprenoid biosynthesis.

Biochemistry

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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

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  1. ^ 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.
  2. ^ 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.