5VYW

Crystal structure of Lactococcus lactis pyruvate carboxylase

  • Classification: LIGASE
  • Expression System: Escherichia coli

  • Deposited: 2017-05-26 Released: 2017-08-16 
  • Deposition Author(s): Choi, P.H., Tong, L.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1073/pnas.1704756114
  • Primary Citation of Related Structures:  

  • 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 mon ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate carboxylase
A, B, C, D
1143N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
BTN
Query on BTN

Download SDF File 
Download CCD File 
A
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 139.664α = 90.00
b = 139.664β = 90.00
c = 610.490γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-26 
  • Released Date: 2017-08-16 
  • Deposition Author(s): Choi, P.H., Tong, L.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI116669

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Database references