User:Andrea Bauer/Sandbox 956

3N0F is a two chain structure originated at Populus tremula x populus alba. It is an enzyme for isoprene production, present in most of tree species. It is not yet fully understood how plants benefit from isoprene synthesis.
Related:	3n0g
Cofactors:	3 Mg2+ (Not shown on model)
Gene:	ispS (Populus tremula x Populus alba)
Activity:	Isoprene synthase, with EC number 4.2.3.27
Resources:	FirstGlance, OCA, RCSB, PDBsum
Evolutionary Conservation:	Click to display evolutionary Conservation according to ConSurfDB.

Description

Isoprene Synthase is supposed to be a dimeric enzyme which consists of 595 amino acids and has a molecular mass of 68,386 Da. The protein is made up of alpha-helices which form two alpha-helical domains.^[1] The of the protein chain is folded similar to class II terpenoid synthases that are made up of (𝛼𝛼)6 barrels ^[2]. Up to now there is no catalytic activity known for this domain. Quite the contrary regarding the of the isoprene synthase: This domain shows up an 𝛼-helical class I terpenoid synthase fold and contains the active site which is surrounded by five 𝛼-helices. The active site of the enzyme is located in a deep hydrophobic pocket which ensures a protection of the reaction intermediate from water.^[1]

Catalyzed Reaction

The Isoprene Synthase catalyses the production of isoprene from the substrate dimethylallyl-diphosphate (DMAPP)[1]. During the reaction inorganic pyrophosphate is eliminated leading to the reaction products isoprene and inorganic pyrophosphate. The release of the pyrophosphate group leads to the generation of an allylic carbocation which is typical of class I terpenoid syntheses^[2]. The occuring elimination mechanism is syn-periplanar and the leaving diphpsphate group acts as general base. The characteristic DDXXD-sequence motif of class I terpenoid synthases that binds to the diphosphate leaving group via Mg2+-ions facilitates the release of the pyrophosphate group.^[1]

Structure

The hydrophobic active site pocket has a higher affinity towards a 5-carbon substrate rather than to a 10-carbon complex and Van der Waals interactions take place with DMASPP (DMAPP analogous substrate) and the isoprenoid of the active site on F338, V341 and F485. PcISPS remains in the open conformation while being in the DMASPP complex. It was suggested that the diphosphate leaving group itself serves as general base. So a syn-periplanar elimination reaction was suggested with the development of an intermediate carbocation, which leads to the assumption that the isoprene generation is catalyzed by a substrate-assisted mechanism. PcISPS was found to be monomeric in crystallization. However, positive cooperativity has been observed which is unusual for a monomeric enzyme . There was evidence that this cooperativity results from a dimeric quarternary structure, where C-terminal catalytic domains interact to form an isologous dimer.^[1]

Cofactors

For isoprene synthesis, several mechanisms and metal-binding motifs play an essential role. were found to be conserved like the “aspartate-rich” motif D345DXXD. These metal ions like Mg2+ or Mn2+ are essential for DMAPP diphosphate to be released. PcISPS in fact is the first terpenoid synthase to show up metal binding motifs of terpenoid cyclases. These metal binding motifs have the ability to interact with a trinuclear Mg2+ cluster in complex with DMASPP. Mg2+A binds fully while B and C bind less. This can be considered to occur because of structural geometry in this binding being less good. The PcISPS-DMASPP complex does not show significant conformational changes in regard to the single PcISPS. In addition to interactions with metal ions, the diphosphate group also accepts from R486 and N489. One (monomer A) or two (monomer B) oxygen atoms and also coordinate Mg2+B and Mg2+A.^[1]

Biological Relevance

The interest in the isoprene synthase and especially the mechanism of this enzyme is based on the aim to develop carbon fuels in bioreactors that do not rest upon a petrochemical process. Isoprene can make up a somehow “greener” source for rubber and plastic products.^[1] Furthermore there is a structure-based engineering of terpenoid synthase function to make it accessible to a huge amount of biotechnological applications which are named above.^[3]

References

1. ↑ ^{1.0 1.1 1.2 1.3 1.4 1.5} Koksal M, Zimmer I, Schnitzler JP, Christianson DW. Structure of Isoprene Synthase Illuminates the Chemical Mechanism of Teragram Atmospheric Carbon Emission. J Mol Biol. 2010 Jul 17. PMID:20624401 doi:10.1016/j.jmb.2010.07.009
2. ↑ ^{2.0 2.1} Wendt KU, Schulz GE. Isoprenoid biosynthesis: manifold chemistry catalyzed by similar enzymes. Structure. 1998 Feb 15;6(2):127-33. PMID:9519404
3. ↑ Ghirardo A, Gutknecht J, Zimmer I, Bruggemann N, Schnitzler JP. Biogenic volatile organic compound and respiratory CO2 emissions after 13C-labeling: online tracing of C translocation dynamics in poplar plants. PLoS One. 2011 Feb 28;6(2):e17393. doi: 10.1371/journal.pone.0017393. PMID:21387007 doi:http://dx.doi.org/10.1371/journal.pone.0017393