6KD7

Crystal structure of geranylgeranyl pyrophosphate synthase

Summary for 6KD7

• Entry DOI: 10.2210/pdb6kd7/pdb
• Descriptor: Polyprenyl synthetase, PYROPHOSPHATE, GLYCEROL, ... (5 entities in total)
• Functional Keywords: prenyltransferase, transferase
• Biological source: Nonlabens dokdonensis (strain DSM 17205 / KCTC 12402 / DSW-6)
• Total number of polymer chains: 1
• Total formula weight: 38586.07

Authors

Kim, S.,Kim, K.-J. (deposition date: 2019-07-01, release date: 2019-09-11, Last modification date: 2023-11-22)

Primary citation

Kim, S.,Kim, E.J.,Park, J.B.,Kim, S.W.,Kim, K.J.
Crystal structure of geranylgeranyl pyrophosphate synthase (crtE) from Nonlabens dokdonensis DSW-6.
Biochem.Biophys.Res.Commun., 518:479-485, 2019

PubMed Abstract: Isoprenoids comprise a diverse group of natural products with a broad range of metabolic functions. Isoprenoids are synthesized from prenyl pyrophosphates by prenyltransferases that catalyze the isoprenoid chain-elongation process to different chain lengths. We hereby present the crystal structure of geranylgeranyl pyrophosphate synthase from the marine flavobacterium Nonlabens dokdonensis DSW-6 (NdGGPPS). NdGGPPS forms a hexamer composed of homodimeric trimer, and the monomeric structure is composed of 15 α-helices (α1-α15). In this structure, we observed the binding of one pyrophosphate molecule and two glycerol molecules that mimicked substrate binding to the enzyme. The substrate binding site of NdGGPPS contains large hydrophobic residues such as Phe, His and Tyr, and structural and amino acids sequence analyses thereof suggest that the protein belongs to the short-chain prenyltransferase family.

PubMed: 31427080
DOI: 10.1016/j.bbrc.2019.08.071

Experimental method

X-RAY DIFFRACTION (2 Å)