5VYZ

Crystal structure of Lactococcus lactis pyruvate carboxylase in complex with cyclic-di-AMP

Summary for 5VYZ

• Entry DOI: 10.2210/pdb5vyz/pdb
• Related: 5VYW
• Descriptor: Pyruvate carboxylase, MANGANESE (II) ION, ADENOSINE-5'-DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: biotin-dependent carboxylase tim-barrel cyclic-di-amp, ligase
• Biological source: Lactococcus lactis
• Total number of polymer chains: 4
• Total formula weight: 513249.72

Authors

Choi, P.H.,Tong, L. (deposition date: 2017-05-26, release date: 2017-08-16, Last modification date: 2024-03-13)

Primary citation

Choi, P.H.,Vu, T.M.N.,Pham, H.T.,Woodward, J.J.,Turner, M.S.,Tong, L.
Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria.
Proc. Natl. Acad. Sci. U.S.A., 114:E7226-E7235, 2017

PubMed Abstract: Cyclic di-3',5'-adenosine monophosphate (c-di-AMP) is a broadly conserved bacterial second messenger that has been implicated in a wide range of cellular processes. Our earlier studies showed that c-di-AMP regulates central metabolism in by inhibiting its pyruvate carboxylase (LmPC), a biotin-dependent enzyme with biotin carboxylase (BC) and carboxyltransferase (CT) activities. We report here structural, biochemical, and functional studies on the inhibition of PC (LlPC) by c-di-AMP. The compound is bound at the dimer interface of the CT domain, at a site equivalent to that in LmPC, although it has a distinct binding mode in the LlPC complex. This binding site is not well conserved among PCs, and only a subset of these bacterial enzymes are sensitive to c-di-AMP. Conformational changes in the CT dimer induced by c-di-AMP binding may be the molecular mechanism for its inhibitory activity. Mutations of residues in the binding site can abolish c-di-AMP inhibition. In , LlPC is required for efficient milk acidification through its essential role in aspartate biosynthesis. The aspartate pool in is negatively regulated by c-di-AMP, and high aspartate levels can be restored by expression of a c-di-AMP-insensitive LlPC. LlPC has high intrinsic catalytic activity and is not sensitive to acetyl-CoA activation, in contrast to other PC enzymes.

PubMed: 28808024
DOI: 10.1073/pnas.1704756114

Experimental method

X-RAY DIFFRACTION (2.3 Å)