Phosphoglycerate kinase

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Phosphoglycerate kinase
Phosphoglycerate kinase
Cartoon representation of the PGK, with ATP and PG (in stick representation) and magnesium ion in green. PDB  3PGK

Existing structural data : 2zgv , 3c39 , 3c3a , 3c3b , 3c3c

Properties of human protein
Mass / length primary structure 416 amino acids
Secondary to quaternary structure Monomer
Identifier
Gene names PGK1  ; PGK2
External IDs
Enzyme classification
EC, category 2.7.2.3 ,  kinase
Response type (De-) phosphorylation
Substrate ATP + 3- phospho - D -glycerate
Products ADP + 1,3- bisphospho - D -glycerate
Occurrence
Homology family PGK
Parent taxon Creature

Phosphoglycerate kinase (PGK) is the name for the enzyme that adds a phosphate group to the substance 3-phosphoglycerate . The reverse reaction, the removal of phosphate from 1,3-bisphosphoglycerate , is also catalyzed by PGK and is part of glycolysis , the utilization of carbohydrates in the metabolism of all living things. Mutations in the PGK gene can lead to PGK deficiency and haemolytic anemia in humans .

With the mammals, a second isoform of PGK (PGK2) developed, which is located exclusively in the testes . It is very likely caused by copying the mRNA transcript of the PGK1 gene using reverse transcriptase , a so-called retrogene . PGK2 is only expressed during spermatogenesis , as a replacement for PGK1, whose gene is located on the X chromosome and whose production is therefore dormant in this phase.

The formation of PGK is activated in particular by HIF-1 . Another function of PGK1 outside of glycolysis is as disulfide reductase in the formation of blood vessels in tumors, where it is activated by CXCR4 . PGK1 is therefore also part of signal transduction .

structure

PGK is found in all living organisms and its amino acid sequence has been highly conserved throughout evolution. The enzyme is present as monomer residues 415 before, the two virtually equal domains containing the the N - and C termini correspond to the protein. 3-phosphoglycerate (3-PG) binds to the N -terminus, while the nucleotide substrates MgATP or MgADP bind to the C -terminal domain of the enzyme. This extended two-domain structure is associated with large conformational changes that are similar to those of hexokinase .

The two domains of the protein are separated by a cleft and connected by two α-helices . In the center of each domain there is a 6-stranded, parallel β-sheet, which is surrounded by α-helices. The two lobes can be folded independently, due to the presence of intermediates in the folding pathway with a single folded domain. Although the binding of both substrates triggers a conformational change, it is only when both substrates bind that a domain closure (closure of the active center with the help of the domains) occurs, which leads to the transfer of the phosphate group.

The enzyme tends to exist in the open conformation with short periods of occlusion and catalysis, allowing rapid diffusion of substrate and products through the binding sites. The open conformation of PGK is more conformationally stable due to the exposure of a hydrophobic region of the protein during domain closure .

Role of magnesium

Magnesium ions are usually complexed with the phosphate groups of the nucleotide substrates of PGK. It is known that in the absence of magnesium there is no enzyme activity. The divalent metal helps the enzyme ligands to shield the negative charges of the bound phosphate group, which enables the nucleophilic attack to occur. This charge stabilization is a typical feature of the phosphotransfer reaction. It is believed that the ion also promotes domain closure when PGK has bound both substrates.

Catalyzed equilibrium

Structural formula of D-1,3 bisphosphoglycerate+ ADP ⇔ Structural formula of D-3 phosphoglycerate+ ATP

Phosphate is transferred from 1,3-bisphosphoglycerate to ADP and vice versa.

mechanism

Mechanism of phosphoglycerate kinase in glycolysis.

Without any substrate binding, PGK exists in an “open” conformation. After both the Triose- as well as the nucleotide substrate in the N - and C -terminal domains are attached, enters an extended hinge movement ( hinge-bending motion on), which brings the domains and their bound substrates into close proximity and "closed" to a Conformation leads. In the case of forward glycolysis, the β-phosphate of ADP triggers a nucleophilic attack on the phosphate on the C1 atom of 1,3-BPG. The Lys 219 on the enzyme leads the phosphate group to the substrate.

PGK passes through a charge-stabilized transition state , which is preferred over the arrangement of the bound substrate in the closed enzyme, since in the transition state all three phosphate oxygen atoms are stabilized by ligands, in contrast to only two stabilized oxygen atoms in the bound initial state.

regulation

The enzyme is activated by low concentrations of various polyvalent anions such as pyrophosphate , sulfate , phosphate and citrate . High concentrations of MgATP and 3-PG activate PGK, while Mg 2+ in high concentrations does not inhibit the enzyme competitively.

PGK shows a broad specificity towards nucleotide substrates. Its activity is inhibited by salicylates , which appear to mimic the enzyme's nucleotide substrate.

It has been shown that macromolecular crowding (overfilling a living cell, for example, with macromolecules) increases PGK activity both in computer simulations and in in vitro environments that simulate the interior of the cell. As a result of the overcrowding, the enzyme becomes enzymatically more active and compact.

Clinical significance

PGK deficiency is an X-linked recessive trait that is associated with hemolytic anemia, mental disorders, and myopathy in humans. Depending on the form, there is a hemolytic and a myopathic form of PGK deficiency. Because the trait is X linked, it is usually fully expressed in males with one X chromosome. Affected women are usually asymptomatic (without symptoms). The condition results from mutations in Pgk1, the gene encoding PGK1, and twenty mutations have been identified. At the molecular level, the mutation in Pgk1 affects the thermal stability and inhibits the catalytic activity of the enzyme. PGK is the only enzyme in glycolysis that is encoded by an X-linked gene. In hemolytic anemia, there is a deficiency of PGK in the erythrocytes . There is currently no definitive treatment for PGK deficiency.

An overexpression of PGK1 was gastric cancer associated and it was found that the invasiveness increased gastric cancer cells in vitro. The enzyme is secreted by tumor cells and is involved in angiogenesis , which leads to the release of angiostatin and the inhibition of the growth of tumor blood vessels.

Because of its broad specificity towards nucleotide substrates, PGK is known to be involved in the phosphorylation and activation of HIV antiretroviral agents on a nucleotide basis.

Web links

Wikibooks: Biochemistry and Pathobiochemistry: Phosphoglycerate Kinase  - Learning and Teaching Materials

Individual evidence

  1. ↑ UniProt P00558 .
  2. ↑ PGK2.  In: Online Mendelian Inheritance in Man . (English).
  3. ↑ PGK1.  In: Online Mendelian Inheritance in Man . (English).
  4. ^ J. Wang et al .: A glycolytic mechanism regulating an angiogenic switch in prostate cancer. Cancer Res 67/1 /. 2007 : 149-159; PMID 17210694 .
  5. ↑ a b A. Dhar, A. Samiotakis, S. Ebbinghaus, L. Nienhaus, D. Homouz, M. Gruebele, MS Cheung: Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding. In: Proceedings of the National Academy of Sciences . Volume 107, number 41, October 2010, pp. 17586-17591, doi : 10.1073 / pnas.1006760107 , PMID 20921368 , PMC 2955104 (free full text).
  6. ^ S. Kumar, B. Ma, CJ Tsai, H. Wolfson, R. Nussinov: Folding funnels and conformational transitions via hinge-bending motions. In: Cell biochemistry and biophysics. Volume 31, Number 2, 1999, pp. 141-164, doi : 10.1007 / BF02738169 , PMID 10593256 (review).
  7. ↑ a b c d e L. R. Chiarelli, SM Morera, P. Bianchi, E. Fermo, A. Zanella, A. Galizzi, G. Valentini: Molecular insights on pathogenic effects of mutations causing phosphoglycerate kinase deficiency. In: PLOS ONE . Volume 7, number 2, 2012, p. E32065, doi : 10.1371 / journal.pone.0032065 , PMID 22348148 , PMC 3279470 (free full text).
  8. ↑ a b J. M. Yon, M. Desmadril, JM Betton, P. Minard, N. Ballery, D. Missiakas, S. Gaillard-Miran, D. Perahia, L. Mouawad: Flexibility and folding of phosphoglycerate kinase. In: Biochemistry. Volume 72, Numbers 6-7, 1990 Jun-Jul, pp 417-429, doi : 10.1016 / 0300-9084 (90) 90066-p , PMID 2124145 (review).
  9. ↑ L. Zerrad, A. Merli, MD Schroeder, A. Varga, .. Gráczer, P. Pernot, A. Round, M. Vas, MW Bo: A spring-loaded release mechanism Regulates domain movement and catalysis in phosphoglycerate kinase. In: Journal of Biological Chemistry . Volume 286, Number 16, April 2011, pp. 14040-14048, doi : 10.1074 / jbc.M110.206813 , PMID 21349853 , PMC 3077604 (free full text).
  10. ↑ a b A. Varga, Z. Palmai, Z. Gugolya, .. Gráczer, F. Vonderviszt, P. Závodszky, E. Balog, M .: Importance of aspartate residues in balancing the flexibility and fine-tuning the catalysis of human 3-phosphoglycerate kinase. In: Biochemistry. Volume 51, number 51, December 2012, pp. 10197-10207, doi : 10.1021 / bi301194t , PMID 23231058 .
  11. ↑ MJ Cliff, MW Bowler, A. Varga, JP Marston, J. Szabó, AM Hounslow, NJ Baxter, GM Blackburn, M. Vas, JP Waltho: Transition state analogue structures of human phosphoglycerate kinase establish the importance of charge balance in catalysis . In: Journal of the American Chemical Society . Volume 132, Number 18, May 2010, pp. 6507-6516, doi : 10.1021 / ja100974t , PMID 20397725 .
  12. ↑ RD Banks, CCF Blake, PR Evans, R. Haser, DW Rice, GW Hardy, M. Merrett, AW Phillips: Sequence, structure and activity of phosphoglycerate kinase: a possible hinge-bending enzyme. In: Nature. 279, 1979, p. 773, doi : 10.1038 / 279773a0 .
  13. ^ BE Bernstein, WG Hol: Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism. In: Biochemistry. Volume 37, Number 13, March 1998, pp. 4429-4436, doi : 10.1021 / bi9724117 , PMID 9521762 .
  14. ↑ M. Larsson-Raźnikiewicz: Kinetic studies on the reaction catalyzed by phosphoglycerate kinase. II. The kinetic relationships between 3-phosphoglycerate, MgATP2 and activating metal ion. In: Biochimica et Biophysica Acta . Volume 132, Number 1, January 1967, pp. 33-40, doi : 10.1016 / 0005-2744 (67) 90189-1 , PMID 6030358 .
  15. ↑ a b A. Varga, L. Chaloin, G. Sági, R. Sendula, E. Gráczer, K. Liliom, P. Závodszky, C. Lionne, M. Vas: Nucleotide promiscuity of 3-phosphoglycerate kinase is in focus: implications for the design of better anti-HIV analogues. In: Molecular bioSystems. Volume 7, Number 6, June 2011, pp. 1863-1873, doi : 10.1039 / c1mb05051f , PMID 21505655 .
  16. ↑ Märtha Larsson-Raźnikiewicz, Eva Wiksell: Inhibition of phosphoglycerate kinase by salicylates. In: Biochimica et Biophysica Acta - Enzymology. 523, 1978, p. 94, doi : 10.1016 / 0005-2744 (78) 90012-8 .
  17. ^ A. Yoshida, K. Tani: Phosphoglycerate kinase abnormalities: functional, structural and genomic aspects. In: Biomedica biochimica acta. Volume 42, Numbers 11-12, 1983, pp. S263-S267, PMID 6689547 .
  18. ↑ a b c E. Beutler: PGK deficiency. In: British Journal of Hematology . Volume 136, Number 1, January 2007, pp. 3-11, doi : 10.1111 / j.1365-2141.2006.06351.x , PMID 17222195 (review).
  19. ↑ Phosphoglycerate kinase deficiency. In: Genetics Home Reference. United States National Library of Medicine, October 29, 2019; accessed November 1, 2019 .
  20. ↑ M. Rhodes, L. Ashford, B. Manes, C. Calder, J. Domm, H. Frangoul: Bone marrow transplantation in phosphoglycerate kinase (PGK) deficiency. In: British Journal of Hematology . Volume 152, Number 4, February 2011, pp. 500-502, doi : 10.1111 / j.1365-2141.2010.08474.x , PMID 21223252 .
  21. ↑ D. Zieker, I. Königsrainer, I. Tritschler, M. Löffler, S. Beckert, F. Traub, K. Nieselt, S. Bühler, M. Weller, J. Gaedcke, RS Taichman, H. Northoff, BL Brücher , A. Königsrainer: Phosphoglycerate kinase 1 a promoting enzymes for peritoneal dissemination in gastric cancer. In: International Journal of Cancer . Volume 126, number 6, March 2010, pp. 1513-1520, doi : 10.1002 / ijc.24835 , PMID 19688824 , PMC 2811232 (free full text).
  22. ^ AJ Lay, XM Jiang, O. Kisker, E. Flynn, A. Underwood, R. Condron, PJ Hogg: Phosphoglycerate kinase acts in tumor angiogenesis as a disulphide reductase. In: Nature . Volume 408, Number 6814, December 2000, pp. 869-873, doi : 10.1038 / 35048596 , PMID 11130727 .
  23. ^ S. Gallois-Montbrun, A. Faraj, E. Seclaman, JP Sommadossi, D. Deville-Bonne, M. Véron: Broad specificity of human phosphoglycerate kinase for antiviral nucleoside analogs. In: Biochemical pharmacology. Volume 68, Number 9, November 2004, pp. 1749-1756, doi : 10.1016 / j.bcp.2004.06.012 , PMID 15450940 .