7ZZ3

Cryo-EM structure of "BC react" conformation of Lactococcus lactis pyruvate carboxylase with acetyl-CoA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

CryoEM structural exploration of catalytically active enzyme pyruvate carboxylase.

Lopez-Alonso, J.P.Lazaro, M.Gil-Carton, D.Choi, P.H.Tong, L.Valle, M.

(2022) Nat Commun 13: 6185-6185

  • DOI: https://doi.org/10.1038/s41467-022-33987-2
  • Primary Citation of Related Structures:  
    7ZYY, 7ZYZ, 7ZZ0, 7ZZ1, 7ZZ2, 7ZZ3, 7ZZ4, 7ZZ5, 7ZZ6, 7ZZ8

  • PubMed Abstract: 

    Pyruvate carboxylase (PC) is a tetrameric enzyme that contains two active sites per subunit that catalyze two consecutive reactions. A mobile domain with an attached prosthetic biotin links both reactions, an initial biotin carboxylation and the subsequent carboxyl transfer to pyruvate substrate to produce oxaloacetate. Reaction sites are at long distance, and there are several co-factors that play as allosteric regulators. Here, using cryoEM we explore the structure of active PC tetramers focusing on active sites and on the conformational space of the oligomers. The results capture the mobile domain at both active sites and expose catalytic steps of both reactions at high resolution, allowing the identification of substrates and products. The analysis of catalytically active PC tetramers reveals the role of certain motions during enzyme functioning, and the structural changes in the presence of additional cofactors expose the mechanism for allosteric regulation.


  • Organizational Affiliation

    CIC bioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Bizkaia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate carboxylase
A, B, C, D
1,143Lactococcus lactisMutation(s): 0 
Gene Names: BW154_09950
EC: 6.4.1.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download Ideal Coordinates CCD File 
CA [auth D],
J [auth A],
Q [auth B],
W [auth C]
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
ATP
Query on ATP

Download Ideal Coordinates CCD File 
H [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth D],
O [auth B],
U [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BTN (Subject of Investigation/LOI)
Query on BTN

Download Ideal Coordinates CCD File 
E [auth A]BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
PYR
Query on PYR

Download Ideal Coordinates CCD File 
DA [auth D],
K [auth A],
R [auth B],
X [auth C]
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
L [auth A]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
MN
Query on MN

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B],
T [auth C],
Z [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth D]
F [auth A]
I [auth A]
M [auth B]
P [auth B]
BA [auth D],
F [auth A],
I [auth A],
M [auth B],
P [auth B],
S [auth C],
V [auth C],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2
RECONSTRUCTIONRELION3.1.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Human Frontier Science Program (HFSP)FranceRGP0062/2016
Spanish Ministry of Science, Innovation, and UniversitiesSpainPGC2018-098996-B-100

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Refinement description