6N0Z

Crystal structure of Anaerolinea thermophila mevalonate 5-phosphate decarboxylase N20K H194M mutant complexed with (R)-MVAPP

Summary for 6N0Z

• Entry DOI: 10.2210/pdb6n0z/pdb
• Descriptor: Diphosphomevalonate decarboxylase, (3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID (3 entities in total)
• Functional Keywords: lyase
• Biological source: Anaerolinea thermophila (strain DSM 14523 / JCM 11388 / NBRC 100420 / UNI-1)
• Total number of polymer chains: 6
• Total formula weight: 216365.32

Authors

Noel, J.P.,Thomas, S.T.,Louie, G.V. (deposition date: 2018-11-07, release date: 2019-07-17, Last modification date: 2023-10-11)

Primary citation

Thomas, S.T.,Louie, G.V.,Lubin, J.W.,Lundblad, V.,Noel, J.P.
Substrate Specificity and Engineering of Mevalonate 5-Phosphate Decarboxylase.
Acs Chem.Biol., 14:1767-1779, 2019

PubMed Abstract: A bifurcation of the mevalonate (MVA) pathway was recently discovered in bacteria of the Chloroflexi phylum. In this alternative route for the biosynthesis of isopentenylpyrophosphate (IPP), the penultimate step is the decarboxylation of ()-mevalonate 5-phosphate (()-MVAP) to isopentenyl phosphate (IP), which is followed by the ATP-dependent phosphorylation of IP to IPP catalyzed by isopentenyl phosphate kinase (IPK). Notably, the decarboxylation reaction is catalyzed by mevalonate 5-phosphate decarboxylase (MPD), which shares considerable sequence similarity with mevalonate diphosphate decarboxylase (MDD) of the classical MVA pathway. We show that an enzyme originally annotated as an MDD from the Chloroflexi bacterium possesses equal catalytic efficiency for ()-MVAP and ()-mevalonate 5-diphosphate (()-MVAPP). Further, the molecular basis for this dual specificity is revealed by near atomic-resolution X-ray crystal structures of MPD/MDD bound to ()-MVAP or ()-MVAPP. These findings, when combined with sequence and structural comparisons of this bacterial enzyme, functional MDDs, and several putative MPDs, delineate key active-site residues that confer substrate specificity and functionally distinguish MPD and MDD enzyme classes. Extensive sequence analyses identified functional MPDs in the halobacteria class of archaea that had been annotated as MDDs. Finally, no eukaryotic MPD candidates were identified, suggesting the absence of the alternative MVA (altMVA) pathway in all eukaryotes, including, paradoxically, plants, which universally encode a structural and functional homologue of IPK. Additionally, we have developed a viable engineered strain of as an metabolic model and a synthetic biology platform for enzyme engineering and terpene biosynthesis in which the classical MVA pathway has been replaced with the altMVA pathway.

PubMed: 31268677
DOI: 10.1021/acschembio.9b00322

Experimental method

X-RAY DIFFRACTION (1.95 Å)