PDBsum entry 4qg9

Transferase

PDB id: 4qg9

Contents

Protein chains

499 a.a.

417 a.a.

Ligands

ACT ×4

Metals

_MG ×3

Waters ×448

PDB id:

4qg9

Name:

Transferase

Title:

Crystal structure of pkm2-r399e mutant

Structure:

Pyruvate kinase pkm. Chain: a, b, c, d. 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. Mutation: yes

Source:

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

Resolution:

2.38Å R-factor: 0.212 R-free: 0.256

Authors:

P.Wang,C.Sun,T.Zhu,Y.Xu

Key ref:

P.Wang et al. (2015). Structural insight into mechanisms for dynamic regulation of PKM2. Protein Cell, 6, 275-287. PubMed id: 25645022 DOI: 10.1007/s13238-015-0132-x

Date:

22-May-14 Release date: 25-Feb-15

Protein chains

P14618  (KPYM_HUMAN) -  Pyruvate kinase PKM from Homo sapiens

Seq: 531 a.a.

Struc: 499 a.a.*

Protein chains

P14618  (KPYM_HUMAN) -  Pyruvate kinase PKM from Homo sapiens

Seq: 531 a.a.

Struc: 417 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D: E.C.2.7.1.40 - pyruvate kinase.
• Reaction: pyruvate + ATP = phosphoenolpyruvate + ADP + H⁺

pyruvate + ATP (Bound ligand (Het Group name = ACT) matches with 66.67% similarity) = phosphoenolpyruvate + ADP + H(+)

• Enzyme class 3: Chains A, B, C, D: 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: Chains A, B, C, D: 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: 10.1007/s13238-015-0132-x

Protein Cell 6:275-287 (2015)

PubMed id: 25645022

Structural insight into mechanisms for dynamic regulation of PKM2.

P.Wang, C.Sun, T.Zhu, Y.Xu.

ABSTRACT

Pyruvate kinase isoform M2 (PKM2) converts phosphoenolpyruvate (PEP) to pyruvate and plays an important role in cancer metabolism. Here, we show that post-translational modifications and a patient-derived mutation regulate pyruvate kinase activity of PKM2 through modulating the conformation of the PKM2 tetramer. We determined crystal structures of human PKM2 mutants and proposed a "seesaw" model to illustrate conformational changes between an inactive T-state and an active R-state tetramers of PKM2. Biochemical and structural analyses demonstrate that PKM2(Y105E) (phosphorylation mimic of Y105) decreases pyruvate kinase activity by inhibiting FBP (fructose 1,6-bisphosphate)-induced R-state formation, and PKM2(K305Q) (acetylation mimic of K305) abolishes the activity by hindering tetramer formation. K422R, a patient-derived mutation of PKM2, favors a stable, inactive T-state tetramer because of strong intermolecular interactions. Our study reveals the mechanism for dynamic regulation of PKM2 by post-translational modifications and a patient-derived mutation and provides a structural basis for further investigation of other modifications and mutations of PKM2 yet to be discovered.