3U2Z | pdb_00003u2z

Activator-Bound Structure of Human Pyruvate Kinase M2

• PDB DOI: https://doi.org/10.2210/pdb3U2Z/pdb

• Classification: transferase/transferase activator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-04 Released: 2012-09-12 
• Deposition Author(s): Hong, B., Dimov, S., Tempel, W., Auld, D., Thomas, C., Boxer, M., Jianq, J.-K., Skoumbourdis, A., Min, S., Southall, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Inglese, J., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis.

Anastasiou, D., Yu, Y., Israelsen, W.J., Jiang, J.K., Boxer, M.B., Hong, B.S., Tempel, W., Dimov, S., Shen, M., Jha, A., Yang, H., Mattaini, K.R., Metallo, C.M., Fiske, B.P., Courtney, K.D., Malstrom, S., Khan, T.M., Kung, C., Skoumbourdis, A.P., Veith, H., Southall, N., Walsh, M.J., Brimacombe, K.R., Leister, W., Lunt, S.Y., Johnson, Z.R., Yen, K.E., Kunii, K., Davidson, S.M., Christofk, H.R., Austin, C.P., Inglese, J., Harris, M.H., Asara, J.M., Stephanopoulos, G., Salituro, F.G., Jin, S., Dang, L., Auld, D.S., Park, H.W., Cantley, L.C., Thomas, C.J., Vander Heiden, M.G.

(2012) Nat Chem Biol 8: 839-847

• PubMed: 22922757 
• DOI: https://doi.org/10.1038/nchembio.1060
• Primary Citation Related Structures: 
  3ME3, 3U2Z


• PubMed Abstract: 
  

  Cancer cells engage in a metabolic program to enhance biosynthesis and support cell proliferation. The regulatory properties of pyruvate kinase M2 (PKM2) influence altered glucose metabolism in cancer. The interaction of PKM2 with phosphotyrosine-containing proteins inhibits enzyme activity and increases the availability of glycolytic metabolites to support cell proliferation. This suggests that high pyruvate kinase activity may suppress tumor growth. We show that expression of PKM1, the pyruvate kinase isoform with high constitutive activity, or exposure to published small-molecule PKM2 activators inhibits the growth of xenograft tumors. Structural studies reveal that small-molecule activators bind PKM2 at the subunit interaction interface, a site that is distinct from that of the endogenous activator fructose-1,6-bisphosphate (FBP). However, unlike FBP, binding of activators to PKM2 promotes a constitutively active enzyme state that is resistant to inhibition by tyrosine-phosphorylated proteins. These data support the notion that small-molecule activation of PKM2 can interfere with anabolic metabolism.

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Organizational Affiliation: 
• Department of Medicine, Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 234.75 kDa 
• Atom Count: 15,896 
• Modeled Residue Count: 2,063 
• Deposited Residue Count: 2,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase isozymes M1/M2	A, B, C, D	533	Homo sapiens	Mutation(s): 0  Gene Names: PKM2, OIP3, PK2, PK3, PKM EC: 2.7.1.40 (PDB Primary Data), 2.7.11.1 (UniProt), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens) Explore P14618  Go to UniProtKB:  P14618
PHAROS:  P14618 GTEx:  ENSG00000067225

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
07T	L [auth B], T [auth C]	6-(3-aminobenzyl)-4-methyl-2-methylsulfinyl-4,6-dihydro-5H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-5-one C17 H16 N4 O2 S2 ZWKJWVSEDISQIS-RUZDIDTESA-N
FBP	E [auth A], M [auth B], S [auth C], Y [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N
UNX	AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Z [auth D]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33u2z

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.762	α = 90
b = 151.163	β = 102.94
c = 93.213	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Hong, B., Dimov, S., Tempel, W., Auld, D., Thomas, C., Boxer, M., Jianq, J.-K., Skoumbourdis, A., Min, S., Southall, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Inglese, J., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary