7ZZ3 | pdb_00007zz3

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

PDB DOI: https://doi.org/10.2210/pdb7ZZ3/pdb
EM Map EMD-15033: EMDB EMDataResource

Classification: LIGASE
Organism(s): Lactococcus lactis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-25 Released: 2022-10-12
Deposition Author(s): Lopez-Alonso, J.P., Lazaro, M., Gil, D., Choi, P.H., Tong, L., Valle, M.
Funding Organization(s): Human Frontier Science Program (HFSP), Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

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

Starting Model: experimental
View more details

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

PubMed: 36261450 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-33987-2
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 515.5 kDa
Atom Count: 34,427
Modeled Residue Count: 4,311
Deposited Residue Count: 4,572
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate carboxylase	A, B, C, D	1,143	Lactococcus lactis	Mutation(s): 0 Gene Names: BW154_09950 EC: 6.4.1.1

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO Query on ACO Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain J [auth A] SDF format, chain CA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain J [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain J [auth A] mmCIF format, chain CA [auth D]	CA [auth D], J [auth A], Q [auth B], W [auth C]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain CA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain W [auth C]
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain AA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain AA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain AA [auth D]	AA [auth D], O [auth B], U [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth D] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain O [auth B] Focus chain U [auth C]
BTN (Subject of Investigation/LOI) Query on BTN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PYR Query on PYR Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain X [auth C] SDF format, chain R [auth B] SDF format, chain K [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain R [auth B] MOL2 format, chain K [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain R [auth B] mmCIF format, chain K [auth A]	DA [auth D], K [auth A], R [auth B], X [auth C]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain X [auth C]
BCT Query on BCT Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Z [auth D] SDF format, chain T [auth C] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B]	G [auth A], N [auth B], T [auth C], Z [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] SDF format, chain V [auth C] SDF format, chain F [auth A] SDF format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain V [auth C] MOL2 format, chain F [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain V [auth C] mmCIF format, chain F [auth A] mmCIF format, chain BA [auth D]	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		Interactions Focus chain BA [auth D] Focus chain F [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth D] Focus chain F [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth C] Focus chain Y [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B, C, D	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2
RECONSTRUCTION	RELION	3.1.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Human Frontier Science Program (HFSP)	France	RGP0062/2016
Spanish Ministry of Science, Innovation, and Universities	Spain	PGC2018-098996-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