Triose Phosphate Isomerase Structure & Mechanism

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Ribbon drawing for one chain of the "TIM barrel" fold
Ribbon drawing for one chain of the "TIM barrel" fold

Contents

General Information

Triose phosphate isomerase (TIM)[1][2] (PDB 1wyi and 1hti) is a crucial enzyme in the glycolytic pathway. reversibly converts the aldose Glyceraldehyde-3-phosphate (GAP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate. Triose phosphate isomerase is not directly regulated, but the enzyme two steps before it in the glycolytic pathway, phosphofructokinase, is a heavily regulated, irreversible enzyme.

Structural Characteristics

The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. The tertiary structure is a , and it is the prototypical example of the "TIM barrel" fold (see ribbon drawing). The quaternary structure is a homodimer. The molecular weight of the enzyme is estimated at 57,400 Da.[3]

Mechanism

The enzyme aids in catalysis by binding tightly to the enediol transition state. To convert GAP to the enediol intermediate, a proton is abstracted from C2 by a base and the carbonyl oxygen atom is protonated by an acid.[4] The enediol intermediate is negatively charged, but is somewhat [5] Mutation of Lys 12 to Arg increases Km by a factor of 22 and decreases Vmax by a factor of 180.[5] To convert the enediol intermediate to DHAP, C1 is protonated by Glu 165, with His 95 removing a proton from C2’s OH group. As a result, the catalytic groups are back to their original states, and catalysis is complete. With GAP as a substrate, Km for the reaction is .34 mM and Vmax is 7200 units/mg protein at 25 degrees C and pH 7.5.[3]

Mechanism of Triose phosphate isomerase. Created by Christian Krenk using Spartan 08.
Mechanism of Triose phosphate isomerase. Created by Christian Krenk using Spartan 08.

An interesting part of the enzyme is the that stabilizes the enediol-like transition state. The flexible loop (residues 167-176)[6] closes over the active site like a hinged lid when substrate is bound, thus preventing phosphate from leaving. A four-residue segment of the loop H-bonds with the phosphate group of the substrate.[4] Without the loop, the enediol intermediate would eliminate phosphate, with the end products being inorganic phosphate and toxic methylglyoxal.[4]



Human triosephosphate isomerase, 1wyi
Activity: Triose-phosphate isomerase, with EC number 5.3.1.1
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml




Human triosephosphate isomerase complex with phosphoglycolic acid 1hti
Ligands:
Activity: Triose-phosphate isomerase, with EC number 5.3.1.1
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



3D structures of triose phosphate isomerase

Triose Phosphate Isomerase

Additional Resources

For additional information, see: Carbohydrate Metabolism

References

  1. Kinoshita T, Maruki R, Warizaya M, Nakajima H, Nishimura S. Structure of a high-resolution crystal form of human triosephosphate isomerase: improvement of crystals using the gel-tube method. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Apr 1;61(Pt, 4):346-9. Epub 2005 Mar 24. PMID:16511037 doi:10.1107/S1744309105008341
  2. Mande SC, Mainfroid V, Kalk KH, Goraj K, Martial JA, Hol WG. Crystal structure of recombinant human triosephosphate isomerase at 2.8 A resolution. Triosephosphate isomerase-related human genetic disorders and comparison with the trypanosomal enzyme. Protein Sci. 1994 May;3(5):810-21. PMID:8061610
  3. 3.0 3.1 Dabrowska A, Kamrowska I, Baranowski T. Purification, crystallization and properties of triosephosphate isomerase from human skeletal muscle. Acta Biochim Pol. 1978;25(3):247-56. PMID:752201
  4. 4.0 4.1 4.2 Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.
  5. 5.0 5.1 Lodi PJ, Chang LC, Knowles JR, Komives EA. Triosephosphate isomerase requires a positively charged active site: the role of lysine-12. Biochemistry. 1994 Mar 15;33(10):2809-14. PMID:8130193
  6. Lolis E, Petsko GA. Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis. Biochemistry. 1990 Jul 17;29(28):6619-25. PMID:2204418

7. Wierenga RK, Kapetaniou EG, Venkatesan R. Triosephosphate isomerase: a highly evolved biocatalyst. Cellular and Molecular Life Sciences. 2010 August 7 67:3961-3982. PMID: 20694739 [1]

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