8U0M

Crystal structure of isopentenyl phosphate kinase from Thermococcus paralvinellae bound to (E)-2-methylbut-2-en-1-yl monophosphate and ATP

Summary for 8U0M

• Entry DOI: 10.2210/pdb8u0m/pdb
• Descriptor: Isopentenyl phosphate kinase, ADENOSINE-5'-DIPHOSPHATE, (2E)-2-methylbut-2-en-1-yl dihydrogen phosphate, ... (5 entities in total)
• Functional Keywords: alternate mevalonate pathway ipk amino acid kinase isoprenoids, transferase
• Biological source: Thermococcus paralvinellae
• Total number of polymer chains: 2
• Total formula weight: 65192.32

Authors

Singh, S.,Thomas, L.M.,Johnson, B.P.,Brown, S. (deposition date: 2023-08-29, release date: 2024-02-21, Last modification date: 2024-06-12)

Primary citation

Johnson, B.P.,Mandal, P.S.,Brown, S.M.,Thomas, L.M.,Singh, S.
Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non-natural substrate specificity.
Proteins, 92:808-818, 2024

PubMed Abstract: Isopentenyl phosphate kinases (IPKs) have recently garnered attention for their central role in biocatalytic "isoprenol pathways," which seek to reduce the synthesis of the isoprenoid precursors to two enzymatic steps. Furthermore, the natural promiscuity of IPKs toward non-natural alkyl-monophosphates (alkyl-Ps) as substrates has hinted at the isoprenol pathways' potential to access novel isoprenoids with potentially useful activities. However, only a handful of IPK crystal structures have been solved to date, and even fewer of these contain non-natural substrates bound in the active site. The current study sought to elucidate additional ternary complexes bound to non-natural substrates using the IPK homolog from Thermococcus paralvinellae (TcpIPK). Four such structures were solved, each bound to a different non-natural alkyl-P and the phosphoryl donor substrate/product adenosine triphosphate (ATP)/adenosine diphosphate (ADP). As expected, the quaternary, tertiary, and secondary structures of TcpIPK closely resembled those of IPKs published previously, and kinetic analysis of a novel alkyl-P substrate highlighted the potentially dramatic effects of altering the core scaffold of the natural substrate. Even more interesting, though, was the discovery of a trend correlating the position of two α helices in the active site with the magnitude of an IPK homolog's reaction rate for the natural reaction. Overall, the current structures of TcpIPK highlight the importance of continued structural analysis of the IPKs to better understand and optimize their activity with both natural and non-natural substrates.

PubMed: 38333996
DOI: 10.1002/prot.26674

Experimental method

X-RAY DIFFRACTION (2.54 Å)