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

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria.

Choi, P.H.Vu, T.M.N.Pham, H.T.Woodward, J.J.Turner, M.S.Tong, L.

(2017) Proc Natl Acad Sci U S A 114: E7226-E7235

  • DOI: https://doi.org/10.1073/pnas.1704756114
  • Primary Citation of Related Structures:  
    5VYW, 5VYZ, 5VZ0

  • 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 Listeria monocytogenes 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 Lactococcus lactis 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 L. lactis , LlPC is required for efficient milk acidification through its essential role in aspartate biosynthesis. The aspartate pool in L. lactis 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.

  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate carboxylase
A, B, C, D
1,145Lactococcus lactisMutation(s): 0 
Gene Names: pycALG36_0614
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2BA

Download Ideal Coordinates CCD File 
H [auth A],
O [auth D]
(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide
C20 H24 N10 O12 P2
Query on ADP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
Q [auth D]
C10 H15 N5 O10 P2
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
P [auth D]
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
N [auth C],
R [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.27α = 66.08
b = 130.431β = 89.05
c = 133.367γ = 70.6
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary