Sandbox341
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| 3hyq, resolution 1.52Å () | |||||||||
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| Non-Standard Residues: | |||||||||
| Gene: | idi (Salmonella enterica subsp. enterica serovar Typhimurium) | ||||||||
| Activity: | Isopentenyl-diphosphate Delta-isomerase, with EC number 5.3.3.2 | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum, TOPSAN | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
INTRODUCTION
This is a image of 3hq
Isoprenoid compounds are the most diverse family of metabolites that are found in nature(1). Here we look at IPP isomerase it's activity is found in a large number of essential processes and is a central posistion in terpenoid biosynthesis(1).IPP can be isomerized to DMAPP by Isopentenyl diphosphate(IDI)isomerase; which is a metal-ion requiring enzyme(3) utilizing mg or mn.
MECHANISM
The biological role of Isopentenyl diphosphate-dimethylallyl diphosphate Isomerase is to catalyze the interconversion of IPP and DMAPP(2).The mechanism of isomerization invovles an elecrophilic attack by a proton from the aqueous medium on the IPP double bond this produces a carbocation which is stabalized by the elimination of the C-2 pro-R hydrogen of IPP(1).The proposed model for this suggests the allyl moeity of IPP fits in a deeply buried cavity with E116 and C67 lying on opposite faces of the substrate within the active site, and closed by W161, Y104, and S36(2).
STRUCTURE
IPP isomerase is composed of 182 amino acids and folds into a globular protein(2). Conformational changes create a distorted octohedral metal cordination site composed of residues H25, H32, H69, E114, and E116(2).As stated above the enzyme requires metal co-factors in the active site; which also consists of Cys and Glu catalytic residues(1). Studies show that the enzyme Km at the optimal pH 6.3 and the pI between 6.0-6.2 is 2.7iM and the Molecular weight is roughly 82 500(1).The size of the mammalian enzyme is 22kDa(1)
REFRENCES
1. Heijden,Robert Van Der.,Ramos-Valdivia,Ana C.,Verpoorte,Robert.(1997).Isopentenyl diphosphate isomerase:a core enzyme in isoprenoid biosynthesis.A review of its biochemistry and function.Natural products reports.pp591-602.
2. Caillet,Joel et al.(2001).Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase.The EMBO journal.Vol20.No7.pp1531-1537.
3. Auria'D,John C et al.(2008).The Arabidopsis thaliana Type 1 Isopentenyl Diphosphate Isomerases Are Targeted to Multiple Subcellular Compartments and Have overlapping functions in Isoprenoid Biosynthesis.The Plant Cell.Vol29.pp677-696.
4. Hemmi,Hisashi.(2004).Type 2 isopentenyl diphosphate isomerase from a thermoacidophilic archaeon Sulfolobus shibatae.Eur j biochem.271.pp1087-1093.