Summary: Phosphoglycerate kinase
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Phosphoglycerate kinase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
Structure of yeast phosphoglycerate kinase.
Phosphoglycerate kinase (EC 188.8.131.52) (PGK) is an enzyme that catalyzes the reversible transfer of a phosphate group from 1,3-bisphosphoglycerate (1,3-BPG) to ADP producing 3-phosphoglycerate (3-PG) and ATP. Like all kinases it is a transferase. PGK is a major enzyme used in glycolysis, in the first ATP-generating step of the glycolytic pathway. In gluconeogenesis, the reaction catalyzed by PGK proceeds in the opposite direction, generating ADP and 1,3-BPG.
In humans, two isozymes of PGK have been so far identified, PGK1 and PGK2. The isozymes have 87-88% identical amino acid sequence identity and though they are structurally and functionally similar, they have different localizations: PGK2, encoded by an autosomal gene, is unique to meiotic and postmeiotic spermatogenic cells, while PGK1, encoded on the X-chromosome, is ubiquitously expressed in all cells.
PGK is present in all living organisms as one of the two ATP-generating enzymes in glycolysis. In the gluconeogenic pathway, PGK catalyzes the reverse reaction. Under biochemical standard conditions, the glycolytic direction is favored.
PGK has been reported to exhibit thiol reductase activity on plasmin, leading to angiostatin formation, which inhibits angiogenesis and tumor growth. The enzyme was also shown to participate in DNA replication and repair in mammal cell nuclei.
The human isozyme PGK2, which is only expressed during spermatogenesis, was shown to be essential for sperm function in mice.
Interactive pathway map
Click on genes, proteins and metabolites below to link to respective articles. [Â§ 1]
- The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534".
PGK is found in all living organisms and its sequence has been highly conserved throughout evolution. The enzyme exists as a 415-residue monomer containing two nearly equal-sized domains that correspond to the N- and C-termini of the protein. 3-phosphoglycerate (3-PG) binds to the N-terminal, 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-scale 'hinge-bending' conformational changes, similar to those found in hexokinase. The two domains of the protein are separated by a cleft and linked by two alpha-helices. At the core of each domain is a 6-stranded parallel beta-sheet surrounded by alpha helices. The two lobes are capable of folding independently, consistent with the presence of intermediates on the folding pathway with a single domain folded. Though the binding of either substrate triggers a conformational change, only through the binding of both substrates does domain closure occur, leading to the transfer of the phosphate group.
The enzyme has a tendency to exist in the open conformation with short periods of closure and catalysis, which allow for 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 upon domain closure.
Role of magnesium
Magnesium ions are normally complexed to the phosphate groups the nucleotide substrates of PGK. It is known that in the absence of magnesium, no enzyme activity occurs. The bivalent metal assists the enzyme ligands in shielding the bound phosphate group's negative charges, allowing the nucleophilic attack to occur; this charge-stabilization is a typical characteristic of phosphotransfer reaction. It is theorized that the ion may also encourage domain closure when PGK has bound both substrates.
Without either substrate bound, PGK exists in an "open" conformation[disambiguation needed]. After both the triose and nucleotide substrates are bound to the N- and C-terminal domains, respectively, an extensive hinge-bending motion occurs, bringing the domains and their bound substrates into close proximity and leading to a "closed" conformation. Then, in the case of the forward glycolytic reaction, the beta-phosphate of ADP initiates a nucleophilic attack on the 1-phosphate of 1,3-BPG in an SN2 substitution reaction. The Lys219 on the enzyme guides the phosphate group to the substrate.
PGK proceeds through a charge-stabilized transition state that is favored over the arrangement of the bound substrate in the closed enzyme because in the transition state, all three phosphate oxygens are stabilized by ligands, as opposed to only two stabilized oxygens in the initial bound state.
In the glycolytic pathyway, 1,3-BPG is the phosphate donor and has a high phosphoryl-transfer potential. The PGK-catalyzed transfer of the phosphate group from 1,3-BPG to ADP to yield ATP can power the carbon-oxidation reaction of the previous glycolytic step (converting glyceraldehyde 3-phosphate to 3-phosphoglycerate).
The enzyme is activated by low concentrations of various multivalent anions, such as pyrophosphate, sulfate, phosphate, and citrate. High concentrations of MgATP and 3-PG activates PGK, while Mg2+ at high concentrations non-competitively inhibits the enzyme.
Macromolecular crowding has been shown to increase PGK activity in both computer simluations and in vitro environments simulating a cell interior; as a result of crowding, the enzyme becomes more enyzmatically active and more compact.
Phosphoglycerate kinase (PGK) deficiency is an X-linked recessive trait associated with hemolytic anemia, mental disorders and myopathy in humans. Since the trait is X-linked, it is usually fully expressed in males, who have one X chromosome; affected females are typically asymptomatic. The condition results from mutations in Pgk1, the gene encoding PGK1, and twenty mutations have been identified. On a molecular level, the mutation in Pgk1 impairs the thermal stability and inhibits the catalytic activity of the enzyme. PGK is the only enzyme in the immediate glycolytic pathway encoded by an X-linked gene. In the case of hemolytic anemia, PGK deficiency occurs in the erythrocytes. Currently, no definitive treatment exists for PGK deficiency.
PGK1 overexpression has been associated with gastric cancer and has been found to increase the invasiveness of gastric cancer cells in vitro. The enzyme is secreted by tumor cells and participates in the angiogenic process, leading to the release of angiostatin and the inhibition of tumor blood vessel growth.
- Watson HC, Walker NP, Shaw PJ et al. (1982). "Sequence and structure of yeast phosphoglycerate kinase". EMBO J. 1 (12): 1635â€“40. PMC 553262. PMID 6765200.
- Chiarelli LR, Morera SM, Bianchi P, Fermo E, Zanella A, Galizzi A, Valentini G (2012). "Molecular insights on pathogenic effects of mutations causing phosphoglycerate kinase deficiency". PLoS ONE 7 (2): e32065. doi:10.1371/journal.pone.0032065. PMC 3279470. PMID 22348148.
- Hogg, Philip J.; Lay, Angelina J.; Jiang, Xing-Mai; Kisker, Oliver; Flynn, Evelyn; Underwood, Anne; Condron, Rosemary (14 December 2000). Nature 408 (6814): 869â€“873. doi:10.1038/35048596. Missing or empty
- Danshina, Polina; GB Geyer; Q Dai; EH Goulding; WD Willis et al. (1 January 2010). "Phosphoglycerate Kinase 2 (PGK2) Is Essential for Sperm Function and Male Fertility in Mice". Biology of Reproduction 82 (1): 136â€“145. doi:10.1095/biolreprod.109.079699.
- Dhar, A.; Samiotakis, A.; Ebbinghaus, S.; Nienhaus, L.; Homouz, D.; Gruebele, M.; Cheung, M. S. (4 October 2010). "Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding". Proceedings of the National Academy of Sciences 107 (41): 17586â€“17591. doi:10.1073/pnas.1006760107.
- Kumar S, Ma B, Tsai CJ, Wolfson H, Nussinov R (1999). "Folding funnels and conformational transitions via hinge-bending motions". Cell Biochem. Biophys. 31 (2): 141â€“64. doi:10.1007/BF02738169. PMID 10593256.
- Yon JM, Desmadril M, Betton JM, Minard P, Ballery N, Missiakas D, Gaillard-Miran S, Perahia D, Mouawad L (1990). "Flexibility and folding of phosphoglycerate kinase". Biochimie 72 (6-7): 417â€“29. doi:10.1016/0300-9084(90)90066-p. PMID 2124145.
- Zerrad L, Merli A, SchrÃ¶der GF, Varga A, GrÃ¡czer Ã‰, Pernot P, Round A, Vas M, Bowler MW (April 2011). "A spring-loaded release mechanism regulates domain movement and catalysis in phosphoglycerate kinase". J. Biol. Chem. 286 (16): 14040â€“8. doi:10.1074/jbc.M110.206813. PMC 3077604. PMID 21349853.
- Varga, Andrea; Palmai, Zoltan; Gugolya, ZoltÃ¡n; GrÃ¡czer, Ã‰va; Vonderviszt, Ferenc; ZÃ¡vodszky, PÃ©ter; Balog, Erika; Vas, MÃ¡ria (21 December 2012). "Importance of Aspartate Residues in Balancing the Flexibility and Fine-Tuning the Catalysis of Human 3-Phosphoglycerate Kinase". Biochemistry 51 (51): 10197â€“10207. doi:10.1021/bi301194t.
- Cliff, MJ; Bowler MW; Varga A; Marston JP et al. (12 May 2010). "Transition state analogue structures of human phosphoglycerate kinase establish the importance of charge balance in catalysis". J Am Chem Soc 132 (18): 6507â€“6516. doi:10.1021/ja100974t. PMID 20397725. Retrieved 6 March 2013.
- Banks, R. D.; Blake, C. C. F.; Evans, P. R.; Haser, R.; Rice, D. W.; Hardy, G. W.; Merrett, M.; Phillips, A. W. (28 June 1979). "Sequence, structure and activity of phosphoglycerate kinase: a possible hinge-bending enzyme". Nature 279 (5716): 773â€“777. doi:10.1038/279773a0.
- "Phosphoglycerate kinase". Mechanism, Annotation and Classification In Enzymes (MACiE). Retrieved 4 March 2013.
- Bernstein, Bradley E; Wim G; Hol J (17 March 1998). "Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism". Biochemistry 37 (13): 4429â€“4436. doi:10.1021/bi9724117.
- Larsson-RaÅºnikiewicz M (January 1967). "Kinetic studies on the reaction catalyzed by phosphoglycerate kinase. II. The kinetic relationships between 3-phosphoglycerate, MgATP2-and activating metal ion". Biochim. Biophys. Acta 132 (1): 33â€“40. doi:10.1016/0005-2744(67)90189-1. PMID 6030358.
- Varga, A; Chaloin K; Sagi G; Sendula R et al. (20 April 2011). "Nucleotide promiscuity of 3-phosphoglycerate kinase is in focus: implications for the design of better anti-HIV analogues". Mol Biosyst 7 (6): 1863â€“73. doi:10.1039/c1mb05051f. PMID 21505655.
- Larsson-RaÅºnikiewicz, MÃ¤rtha; Wiksell, Eva (1 March 1978). "Inhibition of phosphoglycerate kinase by salicylates". Biochimica et Biophysica Acta (BBA) - Enzymology 523 (1): 94â€“100. doi:10.1016/0005-2744(78)90012-8.
- Yoshida A, Tani K (1983). "Phosphoglycerate kinase abnormalities: functional, structural and genomic aspects". Biomed. Biochim. Acta 42 (11-12): S263â€“7. PMID 6689547.
- Beutler E (January 2007). "PGK deficiency". Br. J. Haematol. 136 (1): 3â€“11. doi:10.1111/j.1365-2141.2006.06351.x. PMID 17222195.
- Rhodes, Melissa; Ashford, Linda; Manes, Becky; Calder, Cassie; Domm, Jennifer; Frangoul, Haydar (1 February 2011). "Bone marrow transplantation in phosphoglycerate kinase (PGK) deficiency". British Journal of Haematology 152 (4): 500â€“502. doi:10.1111/j.1365-2141.2010.08474.x.
- Zieker, Derek; KÃ¶nigsrainer, Ingmar; Tritschler, Isabel; LÃ¶ffler, Markus; Beckert, Stefan; Traub, Frank; Nieselt, Kay; BÃ¼hler, Sarah; Weller, Michael; Gaedcke, Jochen; Taichman, Russell S.; Northoff, Hinnak; BrÃ¼cher BL; KÃ¶nigsrainer, Alfred (1 January 2010). "Phosphoglycerate kinase 1 a promoting enzyme for peritoneal dissemination in gastric cancer". International Journal of Cancer: NAâ€“NA. doi:10.1002/ijc.24835.
- Gallois-Mantbrun, Sarah; Faraj A; Seclaman E; Sommadossi JP et al. (1 November 2004). "Broad specificity of human phosphoglycerate kinase for antiviral nucleoside analogs". Biochemical Pharmacology 68 (9): 1749â€“1756. doi:10.1016/j.bcp.2004.06.012. PMID 15450940.
- -858783685 at GPnotebook
- Phosphoglycerate kinase at the US National Library of Medicine Medical Subject Headings (MeSH)
- Illustration at arizona.edu
|Glycolysis Metabolic Pathway|
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
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Internal database links
|SCOOP:||DUF1082 Phage-Gp8 DUF3172|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001576
Phosphoglycerate kinase (EC) (PGK) is an enzyme that catalyses the formation of ATP to ADP and vice versa. In the second step of the second phase in glycolysis, 1,3-diphosphoglycerate is converted to 3-phosphoglycerate, forming one molecule of ATP. If the reverse were to occur, one molecule of ADP would be formed. This reaction is essential in most cells for the generation of ATP in aerobes, for fermentation in anaerobes and for carbon fixation in plants.
PGK is found in all living organisms and its sequence has been highly conserved throughout evolution. The enzyme exists as a monomer containing two nearly equal-sized domains that correspond to the N- and C-termini of the protein (the last 15 C-terminal residues loop back into the N-terminal domain). 3-phosphoglycerate (3-PG) binds to the N-terminal, 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-scale 'hinge-bending' conformational changes, similar to those found in hexokinase [PUBMED:10593256]. At the core of each domain is a 6-stranded parallel beta-sheet surrounded by alpha helices. Domain 1 has a parallel beta-sheet of six strands with an order of 342156, while domain 2 has a parallel beta-sheet of six strands with an order of 321456. Analysis of the reversible unfolding of yeast phosphoglycerate kinase leads to the conclusion that the two lobes are capable of folding independently, consistent with the presence of intermediates on the folding pathway with a single domain folded [PUBMED:2124145].
Phosphoglycerate kinase (PGK) deficiency is associated with haemolytic anaemia and mental disorders in man [PUBMED:6689547].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||phosphoglycerate kinase activity (GO:0004618)|
|Biological process||glycolytic process (GO:0006096)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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|Number in seed:||949|
|Number in full:||21331|
|Average length of the domain:||368.00 aa|
|Average identity of full alignment:||50 %|
|Average coverage of the sequence by the domain:||94.48 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PGK domain has been found. There are 66 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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