Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 252701.23 
• Atom Count: 16136 
• Residue Count: 2268 
• Unique protein chains: 1

1T5A

Human Pyruvate Kinase M2

• DOI: 10.2210/pdb1T5A/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2004-05-03 Released: 2005-07-12 
• Deposition Author(s): Dombrauckas, J.D., Santarsiero, B.D., Mesecar, A.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.278 
• R-Value Work: 0.231 

Literature

Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis.

Dombrauckas, J.D., Santarsiero, B.D., Mesecar, A.D.

(2005) Biochemistry 44: 9417-9429

• PubMed: 15996096 
• DOI: 10.1021/bi0474923


• PubMed Abstract: 
  

Four isozymes of pyruvate kinase are differentially expressed in human tissue. Human pyruvate kinase isozyme M2 (hPKM2) is expressed in early fetal tissues and is progressively replaced by the other three isozymes, M1, R, and L, immediately after birth. In most cancer cells, hPKM2 is once again expressed to promote tumor cell proliferation. Because of its almost ubiquitous presence in cancer cells, hPKM2 has been designated as tumor specific PK-M2, and its presence in human plasma is currently being used as a molecular marker for the diagnosis of various cancers. The X-ray structure of human hPKM2 complexed with Mg(2+), K(+), the inhibitor oxalate, and the allosteric activator fructose 1,6-bisphosphate (FBP) has been determined to a resolution of 2.82 A. The active site of hPKM2 is in a partially closed conformation most likely resulting from a ligand-induced domain closure promoted by the binding of FBP. In all four subunits of the enzyme tetramer, a conserved water molecule is observed on the 2-si face of the prospective enolate and supports the hypothesis that a proton-relay system is acting as the proton donor of the reaction (1). Significant structural differences among the human M2, rabbit muscle M1, and the human R isozymes are observed, especially in the orientation of the FBP-activating loop, which is in a closed conformation when FBP is bound. The structural differences observed between the PK isozymes could potentially be exploited as unique structural templates for the design of allosteric drugs against the disease states associated with the various PK isozymes, especially cancer and nonspherocytic hemolytic anemia.

---

Organizational Affiliation: 

Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60607, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Pyruvate kinase, M2 isozyme	A, B, C, D	567	Homo sapiens	Mutation(s): 0  Gene Names: PKM (OIP3, PK2, PK3, PKM2) EC: 2.7.1.40
Find proteins for P14618 (Homo sapiens) Go to Gene View: PKM Go to UniProtKB:  P14618

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A, B, C, D	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
PO4	A, B, C, D	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	A, B, C, D	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXL	A, B, C, D	OXALATE ION C2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-L
MG	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
FBP	A, B, C, D	BETA-FRUCTOSE-1,6-DIPHOSPHATE FRUCTOSE-1,6-BISPHOSPHATE C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
OXL	Ki: 24000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.278 
• R-Value Work: 0.231 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 108.209	α = 90.00
b = 145.006	β = 90.00
c = 159.260	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
EPMR	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-03 
• Released Date: 2005-07-12 
• Deposition Author(s): Dombrauckas, J.D., Santarsiero, B.D., Mesecar, A.D.

Revision History 

• Version 1.0: 2005-07-12
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance