Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	CryoEM structural exploration of catalytically active enzyme pyruvate carboxylase.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 6185, Year 2022
Publish date	Oct 19, 2022
Authors	Jorge Pedro López-Alonso / Melisa Lázaro / David Gil-Cartón / Philip H Choi / Alexandra Dodu / Liang Tong / Mikel Valle /
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 ...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.
External links	Nat Commun / PubMed:36261450 / PubMed Central
Methods	EM (single particle)
Resolution	2.12 - 3.29 Å
Structure data	15028 7zyy EMDB-15028, PDB-7zyy: Cryo-EM structure of Lactococcus lactis pyruvate carboxylase with acetyl-CoA Method: EM (single particle) / Resolution: 2.12 Å 15029 7zyz EMDB-15029, PDB-7zyz: Cryo-EM structure of "CT oxa" conformation of Lactococcus lactis pyruvate carboxylase with acetyl-CoA Method: EM (single particle) / Resolution: 2.47 Å 15030 7zz0 EMDB-15030, PDB-7zz0: Cryo-EM structure of "CT empty" conformation of Lactococcus lactis pyruvate carboxylase with acetyl-CoA Method: EM (single particle) / Resolution: 2.26 Å 15031 7zz1 EMDB-15031, PDB-7zz1: Cryo-EM structure of "CT react" conformation of Lactococcus lactis pyruvate carboxylase with acetyl-CoA Method: EM (single particle) / Resolution: 2.27 Å 15032 7zz2 EMDB-15032, PDB-7zz2: Cryo-EM structure of "CT pyr" conformation of Lactococcus lactis pyruvate carboxylase with acetyl-CoA Method: EM (single particle) / Resolution: 2.48 Å 15033 7zz3 EMDB-15033, PDB-7zz3: Cryo-EM structure of "BC react" conformation of Lactococcus lactis pyruvate carboxylase with acetyl-CoA Method: EM (single particle) / Resolution: 2.41 Å 15034 7zz4 EMDB-15034, PDB-7zz4: Cryo-EM structure of "BC closed" conformation of Lactococcus lactis pyruvate carboxylase with acetyl-CoA Method: EM (single particle) / Resolution: 2.63 Å 15035 7zz5 EMDB-15035, PDB-7zz5: Cryo-EM structure of "BC open" conformation of Lactococcus lactis pyruvate carboxylase with acetyl-CoA Method: EM (single particle) / Resolution: 2.43 Å 15036 7zz6 EMDB-15036, PDB-7zz6: Cryo-EM structure of "CT-CT dimer" of Lactococcus lactis pyruvate carboxylase with acetyl-CoA Method: EM (single particle) / Resolution: 2.15 Å 15037 7zz8 EMDB-15037, PDB-7zz8: Cryo-EM structure of Lactococcus lactis pyruvate carboxylase with acetyl-CoA and cyclic di-AMP Method: EM (single particle) / Resolution: 3.29 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-MN: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-ACO: ACETYL COENZYME A / Acetyl-CoA ChemComp-PYR: PYRUVIC ACID / Pyruvic acid ChemComp-BCT: BICARBONATE ION / pH bufferYM / Bicarbonate ChemComp-HOH: WATER / Water ChemComp-OAA: OXALOACETATE ION / Oxaloacetic acid ChemComp-BTN: BIOTIN / Biotin ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate ChemComp-2BA: (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
Source	lactococcus lactis (lactic acid bacteria)
Keywords	LIGASE / Tetramer / carboxylase / biotin / inhibitor