5VZ0 | pdb_00005vz0

Crystal structure of Lactococcus lactis pyruvate carboxylase G746A mutant in complex with cyclic-di-AMP

  • Classification: LIGASE
  • Organism(s): Lactococcus lactis
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • 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 (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.218 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5VZ0

Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1073/pnas.1704756114
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 512.63 kDa 
  • Atom Count: 36,604 
  • Modeled Residue Count: 4,488 
  • Deposited Residue Count: 4,576 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyruvate carboxylase
A, B, C, D
1,144Lactococcus lactisMutation(s): 2 
Gene Names: pycALG36_0614
EC: 6.4.1.1

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2BA

Query on 2BA



Download:Ideal Coordinates CCD File
H [auth B],
M [auth C]
(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
PDXMFTWFFKBFIN-XPWFQUROSA-N
ADP

Query on ADP



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B],
O [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
L [auth C],
N [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B],
P [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.218 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.155α = 65.99
b = 130.39β = 88.67
c = 134.271γ = 70.14
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI116669

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: Author supporting evidence, Database references
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary