PDBsum entry 6gg6

Transferase

PDB id: 6gg6

Contents

Protein chains

(+ 2 more) 510 a.a.

Ligands

SER ×8

PO4 ×8

Metals

__K ×8

_MG ×8

PDB id:

6gg6

Name:

Transferase

Title:

Crystal structure of m2 pyk in complex with serine.

Structure:

Pyruvate kinase pkm. Chain: a, b, c, d, e, f, g, h. Synonym: cytosolic thyroid hormone-binding protein,cthbp,opa- interacting protein 3,oip-3,pyruvate kinase 2/3,pyruvate kinase muscle isozyme,thyroid hormone-binding protein 1,thbp1,tumor m2-pk, p58. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pkm, oip3, pk2, pk3, pkm2. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.96Å R-factor: 0.237 R-free: 0.252

Authors:

I.W.Mcnae,M.Yuan,M.D.Walkinshaw

Key ref:

M.Yuan et al. (2018). An allostatic mechanism for M2 pyruvate kinase as an amino-acid sensor. Biochem J, 475, 1821-1837. PubMed id: 29748232 DOI: 10.1042/BCJ20180171

Date:

02-May-18 Release date: 23-May-18

Protein chains

P14618  (KPYM_HUMAN) -  Pyruvate kinase PKM from Homo sapiens

Seq: 531 a.a.

Struc: 510 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: E.C.2.7.1.40 - pyruvate kinase.
• Reaction: pyruvate + ATP = phosphoenolpyruvate + ADP + H⁺

pyruvate + ATP (Bound ligand (Het Group name = SER) matches with 62.50% similarity) = phosphoenolpyruvate + ADP + H(+)

• Enzyme class 3: E.C.2.7.10.2 - non-specific protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺
• Enzyme class 4: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1042/BCJ20180171

Biochem J 475:1821-1837 (2018)

PubMed id: 29748232

An allostatic mechanism for M2 pyruvate kinase as an amino-acid sensor.

M.Yuan, I.W.McNae, Y.Chen, E.A.Blackburn, M.A.Wear, P.A.M.Michels, L.A.Fothergill-Gilmore, T.Hupp, M.D.Walkinshaw.

ABSTRACT

We have tested the effect of all 20 proteinogenic amino acids on the activity of the M2 isoenzyme of pyruvate kinase (M2PYK) and show that, within physiologically relevant concentrations, phenylalanine, alanine, tryptophan, methionine, valine, and proline act as inhibitors, while histidine and serine act as activators. Size exclusion chromatography has been used to show that all amino acids, whether activators or inhibitors, stabilise the tetrameric form of M2PYK. In the absence of amino-acid ligands an apparent tetramer-monomer dissociation K_d is estimated to be ∼0.9 µM with a slow dissociation rate (t_1/2∼15 min). X-ray structures of M2PYK complexes with alanine, phenylalanine, and tryptophan show the M2PYK locked in an inactive T-state conformation, while activators lock the M2PYK tetramer in the active R-state conformation. Amino-acid binding in the allosteric pocket triggers rigid body rotations (11°) stabilising either T or R states. The opposing inhibitory and activating effects of the non-essential amino acids serine and alanine suggest that M2PYK could act as a rapid-response nutrient sensor to rebalance cellular metabolism. This competition at a single allosteric site between activators and inhibitors provides a novel regulatory mechanism by which M2PYK activity is finely tuned by the relative (but not absolute) concentrations of activator and inhibitor amino acids. Such 'allostatic' regulation may be important in metabolic reprogramming and influencing cell fate.