Summary: Phosphoenolpyruvate carboxykinase C-terminal P-loop domain
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Phosphoenolpyruvate carboxykinase Edit Wikipedia article
PDB rendering based on 1khb.
|SCOPe||1khf / SUPFAM|
|phosphoenolpyruvate carboxykinase 1 (soluble)|
|Locus||Chr. 20 q13.31|
|phosphoenolpyruvate carboxykinase 2 (mitochondrial)|
|Alt. symbols||PEPCK-M, PEPCK2|
|Locus||Chr. 14 q12|
Phosphoenolpyruvate carboxykinase (PEPCK) is an enzyme in the lyase family used in the metabolic pathway of gluconeogenesis. It converts oxaloacetate into phosphoenolpyruvate and carbon dioxide.
In humans there are two isoforms of PEPCK; a cytosolic form (SwissProt P35558) and a mitochondrial isoform (SwissProt Q16822) which have 63.4% sequence identity. The cytosolic form is important in gluconeogenesis. However, there is a known transport mechanism to move PEP from the mitochondria to the cytosol, using specific membrane transport proteins.
X-ray structures of PEPCK provide insight into the structure and the mechanism of PEPCK enzymatic activity. The mitochondrial isoform of chicken liver PEPCK complexed with Mn2+, Mn2+-phosphoenolpyruvate (PEP), and Mn2+-GDP provides information about its structure and how this enzyme catalyzes reactions. Delbaere et al. (2004) resolved PEPCK in E. coli and found the active site sitting between a C-terminal domain and an N-terminal domain. The active site was observed to be closed upon rotation of these domains.
Since the eclipsed formation is one that is high in energy, phosphoryl group transfer has a decreased energy of activation, meaning that the groups will transfer more readily. This transfer likely happens via a mechanism similar to SN2 displacement.
In different species
PEPCK gene transcription occurs in many species, and the amino acid sequence of PEPCK is distinct for each species.
As PEPCK acts at the junction between glycolysis and the Krebs cycle, it causes decarboxylation of a C4 molecule, creating a C3 molecule. As the first committed step in gluconeogenesis, PEPCK decarboxylates and phosphorylates oxaloacetate (OAA) for its conversion to PEP, when GTP is present. As a phosphate is transferred, the reaction results in a GDP molecule. When pyruvate kinase - the enzyme that normally catalyzes the reaction that converts PEP to pyruvate - is knocked out in mutants of Bacillus subtilis, PEPCK participates in one of the replacement anaplerotic reactions, working in the reverse direction of its normal function, converting PEP to OAA. Although this reaction is possible, the kinetics are so unfavorable that the mutants grow at a very slow pace or do not grow at all.
PEPCK-C catalyzes an irreversible step of gluconeogenesis, the process whereby glucose is synthesized. The enzyme has therefore been thought to be essential in glucose homeostasis, as evidenced by laboratory mice that contracted diabetes mellitus type 2 as a result of the overexpression of PEPCK-C.
PEPCK-C levels alone were not highly correlated with gluconeogenesis in the mouse liver, as previous studies have suggested. While the mouse liver almost exclusively expresses PEPCK-C, humans equally present a mitochondrial isozyme (PEPCK-M). PEPCK-M has gluconeogenic potential per se. Therefore, the role of PEPCK-C and PEPCK-M in gluconeogenesis may be more complex and involve more factors than was previously believed.
In animals, this is a rate-controlling step of gluconeogenesis, the process by which cells synthesize glucose from metabolic precursors. The blood glucose level is maintained within well-defined limits in part due to precise regulation of PEPCK gene expression. To emphasize the importance of PEPCK in glucose homeostasis, over expression of this enzyme in mice results in symptoms of type II diabetes mellitus, by far the most common form of diabetes in humans. Due to the importance of blood glucose homeostasis, a number of hormones regulate a set of genes (including PEPCK) in the liver that modulate the rate of glucose synthesis.
PEPCK-C is controlled by two different hormonal mechanisms. PEPCK-C activity is increased upon the secretion of both cortisol from the adrenal cortex and glucagon from the alpha cells of the pancreas. Glucagon indirectly elevates the expression of PEPCK-C by increasing the levels of cAMP (via activation of adenylyl cyclase) in the liver which consequently leads to the phosphorylation of S133 on a beta sheet in the CREB protein. CREB then binds upstream of the PEPCK-C gene at CRE (cAMP response element) and induces PEPCK-C transcription. Cortisol on the other hand, when released by the adrenal cortex, passes through the lipid membrane of liver cells (due to its hydrophobic nature it can pass directly through cell membranes) and then binds to a Glucocorticoid Receptor (GR). This receptor dimerizes and the cortisol/GR complex passes into the nucleus where it then binds to the Glucocorticoid Response Element (GRE) region in a similar manner to CREB and produces similar results (synthesis of more PEPCK-C).
Together, cortisol and glucagon can have huge synergistic results, activating the PEPCK-C gene to levels that neither cortisol or glucagon could reach on their own. PEPCK-C is most abundant in the liver, kidney, and adipose tissue.
A collaborative study between the U.S. Environmental Protection Agency (EPA) and the University of New Hampshire investigated the effect of DE-71, a commercial PBDE mixture, on PEPCK enzyme kinetics and determined that in vivo treatment of the environmental pollutant compromises liver glucose and lipid metabolism possibly by activation of the pregnane xenobiotic receptor (PXR), and may influence whole-body insulin sensitivity.
Researchers at Case Western Reserve University have discovered that overexpression of cytosolic PEPCK in skeletal muscle of mice causes them to be more active, more aggressive, and have longer lives than normal mice; see metabolic supermice.
PEPCK (EC 18.104.22.168) is one of three decarboxylation enzymes used in the inorganic carbon concentrating mechanisms of C4 and CAM plants. The others are NADP-malic enzyme and NAD-malic enzyme. In C4 carbon fixation, carbon dioxide is first fixed by combination with phosphoenolpyruvate to form oxaloacetate in the mesophyll. In PEPCK-type C4 plants the oxaloacetate is then converted to aspartate, which travels to the bundle sheath. In the bundle sheath cells, aspartate is converted back to oxaloacetate. PEPCK decarboxylates the bundle sheath oxaloacetate, releasing carbon dioxide, which is then fixed by the enzyme Rubisco. For each molecule of carbon dioxide produced by PEPCK, a molecule of ATP is consumed.
It has also been discovered that, in cucumber (Cucumis sativus L.), PEPCK levels are increased by multiple effects that are known to decrease the cellular pH of plants, although these effects are specific to the part of the plant.
PEPCK levels rose in roots and stems when the plants were watered with ammonium chloride at a low pH (but not at high pH), or with butyric acid. However, PEPCK levels did not increase in leaves under these conditions.
Activity in cancer
PEPCK has not been considered in cancer research until recently. It has been shown that in human tumor samples and human cancer cell lines (breast, colon and lung cancer cells) PEPCK-M, and not PEPCK-C, was expressed at enough levels to play a relevant metabolic role. Therefore, PEPCK-M could have a role in cancer cells, especially under nutrient limitation or other stress conditions.
PEPCK-C is enhanced, both in terms of its production and activation, by many factors. Transcription of the PEPCK-C gene is stimulated by glucagon, glucocorticoids, retinoic acid, and adenosine 3',5'-monophosphate (cAMP), while it is inhibited by insulin. Of these factors, insulin, a hormone that is deficient in the case of type 1 diabetes mellitus, is considered dominant, as it inhibits the transcription of many of the stimulatory elements. PEPCK activity is also inhibited by hydrazine sulfate, and the inhibition therefore decreases the rate of gluconeogenesis.
As discussed previously, PEPCK abundance increased when plants were watered with low-pH ammonium chloride, though high pH did not have this effect.
It is classified under EC number 4.1.1. There are three main types, distinguished by the source of the energy to drive the reaction:
- MÃ©ndez-Lucas A, HyroÅ¡Å¡ovÃ¡ P, Novellasdemunt L, ViÃ±als F, Perales JC (August 2014). "Mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-M) is a pro-survival, endoplasmic reticulum (ER) stress response gene involved in tumor cell adaptation to nutrient availability". J. Biol. Chem. 289 (32): 22090â€“102. doi:10.1074/jbc.M114.566927. PMC 4139223. PMID 24973213.
- MÃ©ndez-Lucas A, Duarte JA, Sunny NE, et al. (July 2013). "PEPCK-M expression in mouse liver potentiates, not replaces, PEPCK-C mediated gluconeogenesis". J. Hepatol. 59 (1): 105â€“13. doi:10.1016/j.jhep.2013.02.020. PMC 3910155. PMID 23466304.
- Chakravarty K, Cassuto H, Reshef L, Hanson RW (2005). "Factors that control the tissue-specific transcription of the gene for phosphoenolpyruvate carboxykinase-C". Critical Reviews in Biochemistry and Molecular Biology. 40 (3): 129â€“54. doi:10.1080/10409230590935479. PMID 15917397.
- Holyoak T, Sullivan SM, Nowak T (July 2006). "Structural insights into the mechanism of PEPCK catalysis". Biochemistry. 45 (27): 8254â€“63. doi:10.1021/bi060269g. PMID 16819824.
- Delbaere LT, Sudom AM, Prasad L, Leduc Y, Goldie H (March 2004). "Structure/function studies of phosphoryl transfer by phosphoenolpyruvate carboxykinase". Biochimica et Biophysica Acta. 1697 (1â€“2): 271â€“8. doi:10.1016/j.bbapap.2003.11.030. PMID 15023367.
- Trapani S, Linss J, Goldenberg S, Fischer H, Craievich AF, Oliva G (November 2001). "Crystal structure of the dimeric phosphoenolpyruvate carboxykinase (PEPCK) from Trypanosoma cruzi at 2 A resolution". Journal of Molecular Biology. 313 (5): 1059â€“72. doi:10.1006/jmbi.2001.5093. PMID 11700062.
- Zamboni N, Maaheimo H, Szyperski T, Hohmann HP, Sauer U (October 2004). "The phosphoenolpyruvate carboxykinase also catalyzes C3 carboxylation at the interface of glycolysis and the TCA cycle of Bacillus subtilis". Metabolic Engineering. 6 (4): 277â€“84. doi:10.1016/j.ymben.2004.03.001. PMID 15491857.
- Vanderbilt Medical Center. "Granner Lab, PEPCK Research." 2001. Online. Internet. Accessed 10:46PM, 4/13/07. www.mc.vanderbilt.edu/root/vumc.php?site=granner&doc=119
- Burgess SC, He T, Yan Z, Lindner J, Sherry AD, Malloy CR, Browning JD, Magnuson MA (April 2007). "Cytosolic phosphoenolpyruvate carboxykinase does not solely control the rate of hepatic gluconeogenesis in the intact mouse liver". Cell Metabolism. 5 (4): 313â€“20. doi:10.1016/j.cmet.2007.03.004. PMC 2680089. PMID 17403375.
- Nash JT; Szabo DT; Carey GB (2012). "Polybrominated diphenyl ethers alter hepatic phosphoenolpyruvate carboxykinase enzyme kinetics in male Wistar rats: implications for lipid and glucose metabolism". Journal of Toxicological and Environmental Health Part A. 76 (2): 142â€“56. doi:10.1080/15287394.2012.738457. PMID 23294302.
- Kanai R, Edwards, GE (1999). "3. The Biochemistry of C4 Photosynthesis". In Sage RF, Monson RK (eds.). C4 Plant Biology. pp. 43â€“87. ISBN 978-0-12-614440-6.CS1 maint: multiple names: authors list (link)
- Christopher JT, Holtum JA (1996). "Patterns of carbon partitioning in leaves of Crassulacean acid metabolism species during deacidification". Plant Physiol. 112 (1): 393â€“399. doi:10.1104/pp.112.1.393. PMC 157961. PMID 12226397.
- Voznesenskaya E.V.; Franceschi V.R.; Chuong S.D.; Edwards G.E. (2006). "Functional characterization of phosphoenolpyruvate carboxykinase-type C4 leaf anatomy: immuno-cytochemical and ultrastructural analyses". Annals of Botany. 98 (1): 77â€“91. doi:10.1093/aob/mcl096. PMC 2803547. PMID 16704997.
- Chen ZH, Walker RP, TÃ©csi LI, Lea PJ, Leegood RC (May 2004). "Phosphoenolpyruvate carboxykinase in cucumber plants is increased both by ammonium and by acidification, and is present in the phloem". Planta. 219 (1): 48â€“58. doi:10.1007/s00425-004-1220-y. PMID 14991407.
- Aich S, Imabayashi F, Delbaere LT (October 2003). "Expression, purification, and characterization of a bacterial GTP-dependent PEP carboxykinase". Protein Expression and Purification. 31 (2): 298â€“304. doi:10.1016/S1046-5928(03)00189-X. PMID 14550651.
- Liu K, Ba X, Yu J, Li J, Wei Q, Han G, Li G, Cui Y (August 2006). "The phosphoenolpyruvate carboxykinase of Mycobacterium tuberculosis induces strong cell-mediated immune responses in mice". Molecular and Cellular Biochemistry. 288 (1â€“2): 65â€“71. doi:10.1007/s11010-006-9119-5. PMID 16691317.
- Leithner K, Hrzenjak A, TrÃ¶tzmÃ¼ller M, et al. (March 2014). "PCK2 activation mediates an adaptive response to glucose depletion in lung cancer". Oncogene. 34 (8): 1044â€“1050. doi:10.1038/onc.2014.47. PMID 24632615.
- O'Brien RM, Lucas PC, Forest CD, Magnuson MA, Granner DK (August 1990). "Identification of a sequence in the PEPCK-C gene that mediates a negative effect of insulin on transcription". Science. 249 (4968): 533â€“7. doi:10.1126/science.2166335. PMID 2166335.
- Mazzio E, Soliman KF (January 2003). "The role of glycolysis and gluconeogenesis in the cytoprotection of neuroblastoma cells against 1-methyl 4-phenylpyridinium ion toxicity". Neurotoxicology. 24 (1): 137â€“47. doi:10.1016/S0161-813X(02)00110-9. PMID 12564389.
- Walter F. Boron (2005). Medical Physiology: A Cellular And Molecular Approach. Elsevier/Saunders. ISBN 978-1-4160-2328-9. Page 858
- Phosphoenolpyruvate+Carboxykinase+(ATP) at the US National Library of Medicine Medical Subject Headings (MeSH)
- Phosphoenolpyruvate+Carboxykinase+(GTP) at the US National Library of Medicine Medical Subject Headings (MeSH)
- "mighty mice" (PEPCK-Cmus mice) http://blog.case.edu/case-news/2007/11/02/mightymouse
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.
Phosphoenolpyruvate carboxykinase C-terminal P-loop domain Provide feedback
Catalyses the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate.
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This tab holds annotation information from the InterPro database.
InterPro entry IPR035077
Phosphoenolpyruvate carboxykinase (PEPCK) catalyses the first committed (rate-limiting) step in hepatic gluconeogenesis, namely the reversible decarboxylation of oxaloacetate to phosphoenolpyruvate (PEP) and carbon dioxide, using either ATP or GTP as a source of phosphate. The ATP-utilising (EC) and GTP-utilising (EC) enzymes form two divergent subfamilies, which have little sequence similarity but which retain conserved active site residues. ATP-utilising PEPCKs are monomers or oligomers of identical subunits found in certain bacteria, yeast, trypanosomatids, and plants, while GTP-utilising PEPCKs are mainly monomers found in animals and some bacteria [PUBMED:16330239]. Both require divalent cations for activity, such as magnesium or manganese. One cation interacts with the enzyme at metal binding site 1 to elicit activation, while the second cation interacts at metal binding site 2 to serve as a metal-nucleotide substrate. In bacteria, fungi and plants, PEPCK is involved in the glyoxylate bypass, an alternative to the tricarboxylic acid cycle.
PEPCK helps to regulate blood glucose levels. The rate of gluconeogenesis can be controlled through transcriptional regulation of the PEPCK gene by cAMP (the mediator of glucagon and catecholamines), glucocorticoids and insulin. In general, PEPCK expression is induced by glucagon, catecholamines and glucocorticoids during periods of fasting and in response to stress, but is inhibited by (glucose-induced) insulin upon feeding [PUBMED:16126724]. With type II diabetes, this regulation system can fail, resulting in increased gluconeogenesis that in turn raises glucose levels [PUBMED:17403375].
PEPCK consists of an N-terminal and a catalytic C-terminal domain, with the active site and metal ions located in a cleft between them. Both domains have an alpha/beta topology that is partly similar to one another [PUBMED:15023367, PUBMED:8609605]. Substrate binding causes PEPCK to undergo a conformational change, which accelerates catalysis by forcing bulk solvent molecules out of the active site [PUBMED:15890557]. PCK uses an alpha/beta/alpha motif for nucleotide binding, this motif differing from other kinase domains. GTP-utilising PEPCK has a PEP-binding domain and two kinase motifs to bind GTP and magnesium.
This entry represents the C-terminal P-loop domain found in GTP-utilising phosphoenolpyruvate carboxykinase enzymes.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||phosphoenolpyruvate carboxykinase activity (GO:0004611)|
|Biological process||gluconeogenesis (GO:0006094)|
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|Seed source:||Pfam-B_1309 (release 2.1)|
|Previous IDs:||PEPCK; PEPCK_C;|
|Number in seed:||200|
|Number in full:||2884|
|Average length of the domain:||344.40 aa|
|Average identity of full alignment:||52 %|
|Average coverage of the sequence by the domain:||58.68 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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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 PEPCK_GTP domain has been found. There are 83 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 sequence.
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