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45  structures 1840  species 1  interaction 2517  sequences 4  architectures

Family: PEPCK (PF00821)

Summary: Phosphoenolpyruvate carboxykinase

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This is the Wikipedia entry entitled "Phosphoenolpyruvate carboxykinase". More...

Phosphoenolpyruvate carboxykinase Edit Wikipedia article

Phosphoenolpyruvate carboxykinase
PBB Protein PCK1 image.jpg
PDB rendering based on 1khb.
Identifiers
Symbol PEPCK
Pfam PF00821
InterPro IPR008209
PROSITE PDOC00421
SCOP 1khf
SUPERFAMILY 1khf
phosphoenolpyruvate carboxykinase 1 (soluble)
Identifiers
Symbol PCK1
Alt. symbols PEPCK-C
Entrez 5105
HUGO 8724
OMIM 261680
RefSeq NM_002591
Other data
Locus Chr. 20 q13.31
phosphoenolpyruvate carboxykinase 2 (mitochondrial)
Identifiers
Symbol PCK2
Alt. symbols PEPCK, PEPCK2
Entrez 5106
HUGO 8725
OMIM 261650
RefSeq NM_001018073
Other data
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.

It is found in two forms, cytosolic and mitochondrial.

Reversibility[edit]

Whereas most reactions of gluconeogenesis can use the glycolysis enzymes in the opposite direction, the pyruvate kinase enzyme is irreversible. The enzymes pyruvate carboxylase and phosphoenolpyruvate carboxykinase provide an alternative path to effectively reverse the actions of pyruvate kinase.

PEPCK in different species[edit]

PEPCK gene transcription occurs in many species, and the amino acid sequence of PEPCK is distinct for each species.

For example, its structure and its specificity differ in humans, Escherichia coli (E. coli), and the parasiteTrypanosoma cruzi.[1]

Animals[edit]

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 is controlled by two different hormonal mechanisms. PEPCK 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 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 gene at CRE (cAMP response element) and induces PEPCK 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).

Together, cortisol and glucagon can have huge synergistic results, activating the PEPCK gene to levels that neither cortisol or glucagon could reach on their own. PEPCK is most abundant in the liver, kidney, and adipose tissue.[2]

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. [3]

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.

Plants[edit]

PEPCK (EC 4.1.1.49) 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.[4][5] 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.

PEPCK acts in plants that undergo C4 carbon fixation, where its action has been localized to the cytosol, in contrast to mammals, where it has been found that PEPCK works in mitochondria.[6]

Although it is found in many different parts of plants, it has been seen only in specific cell types, including the areas of the phloem.[7]

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.[7]

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.

In leaves, 5% CO2 content in the atmosphere leads to higher PEPCK abundance.[7]

Bacteria[edit]

In an effort to explore the role of PEPCK, researchers caused the overexpression of PEPCK in E. coli bacteria via recombinant DNA.[8]

Function in gluconeogenesis[edit]

It has been shown that PEPCK catalyzes the rate-controlling 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.[9]

A recent study suggests that the role that PEPCK plays in gluconeogenesis may be mediated by the citric acid cycle, the activity of which was found to be directly related to PEPCK abundance.[10]

PEPCK levels alone were not found to be highly correlated with gluconeogenesis in the mouse liver, as previous studies have suggested.[10] Therefore, the role of PEPCK in gluconeogenesis may be more complex and involve more factors than was previously believed.

PEPCK of Mycobacterium tuberculosis has been shown to trigger the immune system in mice by increasing cytokine activity.[11]

As a result, it has been found that PEPCK may be an appropriate ingredient in the development of an effective subunit vaccination for tuberculosis.[11]

Structure[edit]

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.[12] 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.[13]

Phosphoryl groups are transferred during PEPCK action, which is likely facilitated by the eclipsed conformation of the phosphoryl groups when ATP is bound to PEPCK.[13]

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.[13]

Reaction Pathway[edit]

PEPCase converts oxaloacetate into phosphoenolpyruvate and carbon dioxide.

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.[12] 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.[14] 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.[14]

In fermentation, PEPCK catalyzes the reaction of PEP and carbon dioxide to OAA, and ADP is therefore converted to ATP with the addition of a phosphate group.[15]

Regulation[edit]

In humans[edit]

PEPCK is enhanced, both in terms of its production and activation, by many factors. Transcription of the PEPCK gene is stimulated by glucagon, glucocorticoids, retinoic acid, and adenosine 3’,5’-monophosphate (cAMP), while it is inhibited by insulin.[16] Of these factors, insulin, a hormone that is deficient in the case of diabetes, is considered dominant, as it inhibits the transcription of many of the stimulatory elements.[16] PEPCK activity is also inhibited by hydrazine sulfate, and the inhibition therefore decreases the rate of gluconeogenesis.[17]

In prolonged acidosis, PEPCK is upregulated in renal proximal tubule brush border cells, in order to secrete more NH3 and thus to produce more HCO3-.[18]

The GTP-specific activity of PEPCK is highest when Mn2+ and Mg2+ are available.[8] In addition, hyper-reactive cysteine (C307) is involved in the binding of Mn2+ to the active site.[12]

Plants[edit]

As discussed previously, PEPCK abundance increased when plants were watered with low-pH ammonium chloride, though high pH did not have this effect.[7]

Classification[edit]

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:

References[edit]

  1. ^ 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): 1059–72. doi:10.1006/jmbi.2001.5093. PMID 11700062. 
  2. ^ 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): 129–54. doi:10.1080/10409230590935479. PMID 15917397. 
  3. ^ 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): 142–56. doi:10.1080/15287394.2012.738457. 
  4. ^ Kanai R, Edwards, GE (1999). "3. The Biochemistry of C4 Photosynthesis". In Sage RF, Monson RK. C4 Plant Biology. pp. 43–87. ISBN 0-12-614440-0. 
  5. ^ Christopher JT, Holtum JAM (1996). "Patterns of carbon partitioning in leaves of Crassulacean acid metabolism species during deacidification". Plant Physiol. 112 (1): 393–399. PMC 157961. PMID 12226397. 
  6. ^ 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): 77–91. 
  7. ^ a b c d Chen ZH, Walker RP, Técsi 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): 48–58. doi:10.1007/s00425-004-1220-y. PMID 14991407. 
  8. ^ a b 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): 298–304. doi:10.1016/S1046-5928(03)00189-X. PMID 14550651. 
  9. ^ 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
  10. ^ a b 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): 313–20. doi:10.1016/j.cmet.2007.03.004. PMC 2680089. PMID 17403375. 
  11. ^ a b 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 (1-2): 65–71. doi:10.1007/s11010-006-9119-5. PMID 16691317. 
  12. ^ a b c Holyoak T, Sullivan SM, Nowak T (July 2006). "Structural insights into the mechanism of PEPCK catalysis". Biochemistry 45 (27): 8254–63. doi:10.1021/bi060269g. PMID 16819824. 
  13. ^ a b c 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 (1-2): 271–8. doi:10.1016/j.bbapap.2003.11.030. PMID 15023367. 
  14. ^ a b 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): 277–84. doi:10.1016/j.ymben.2004.03.001. PMID 15491857. 
  15. ^ Chao YP, Liao JC (February 1994). "Metabolic responses to substrate futile cycling in Escherichia coli". The Journal of Biological Chemistry 269 (7): 5122–6. PMID 8106492. 
  16. ^ a b O'Brien RM, Lucas PC, Forest CD, Magnuson MA, Granner DK (August 1990). "Identification of a sequence in the PEPCK gene that mediates a negative effect of insulin on transcription". Science 249 (4968): 533–7. doi:10.1126/science.2166335. PMID 2166335. 
  17. ^ 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): 137–47. doi:10.1016/S0161-813X(02)00110-9. PMID 12564389. 
  18. ^ Walter F., PhD. Boron. Medical Physiology: A Cellular And Molecular Approaoch. Elsevier/Saunders. ISBN 1-4160-2328-3.  Page 858

External links[edit]

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Phosphoenolpyruvate carboxykinase Provide feedback

Catalyses the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008209

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 GTP-utilising phosphoenolpyruvate carboxykinase enzymes.

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan PEP-carboxyk (CL0374), which has the following description:

This includes the PEP carboxykinase C-terminal domain and HPr kinase HprK C-terminal domain families.

The clan contains the following 3 members:

Hpr_kinase_C PEPCK PEPCK_ATP

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  Seed
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Representative proteomes NCBI
(2002)
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RP15
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RP35
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RP55
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RP75
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  Seed
(56)
Full
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Representative proteomes NCBI
(2002)
Meta
(389)
RP15
(144)
RP35
(249)
RP55
(359)
RP75
(434)
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Curation and family details

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Seed source: Pfam-B_1309 (release 2.1)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 56
Number in full: 2517
Average length of the domain: 325.30 aa
Average identity of full alignment: 56 %
Average coverage of the sequence by the domain: 96.18 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.7 20.7
Trusted cut-off 20.7 20.7
Noise cut-off 20.6 20.6
Model length: 587
Family (HMM) version: 13
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Species distribution

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Interactions

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PEPCK

Structures

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 domain has been found. There are 45 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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