EzCatDB: T00084

DB codeT00084
RLCP classification5.115.3380000.410
3.103.90020.1140
CATH domainDomain 13.40.449.10Catalytic domain
Domain 22.170.8.10Catalytic domain
Domain 33.90.228.20Catalytic domain
E.C.4.1.1.49
CSA1aq2
MACiEM0051


Enzyme Name
Swiss-protKEGG

P22259O09460Q6W6X5Q5SLL5P51058
Protein namePhosphoenolpyruvate carboxykinase {ATP}Phosphoenolpyruvate carboxykinase {ATP}
Phosphoenolpyruvate carboxykinase {ATP}Phosphoenolpyruvate carboxykinase {ATP}, glycosomalphosphoenolpyruvate carboxykinase (ATP)
phosphopyruvate carboxylase (ATP)
phosphoenolpyruvate carboxylase
phosphoenolpyruvate carboxykinase
phosphoenolpyruvate carboxykinase
phosphopyruvate carboxykinase (adenosine triphosphate)
PEP carboxylase
PEP carboxykinase
PEPCK (ATP)
PEPK
PEPCK
phosphoenolpyruvic carboxylase
phosphoenolpyruvic carboxykinase
phosphoenolpyruvate carboxylase (ATP)
phosphopyruvate carboxykinase
ATP:oxaloacetate carboxy-lyase (transphosphorylating)
SynonymsPEP carboxykinase
PEPCK
EC 4.1.1.49
Phosphoenolpyruvate carboxylase
PEP carboxykinase
PEPCK
EC 4.1.1.49
Phosphoenolpyruvate carboxylase
Phosphoenolpyruvate carboxykinase
EC 4.1.1.49
PEP carboxykinase
PEPCK
EC 4.1.1.49
Phosphoenolpyruvate carboxylase
EC 4.1.1.49

KEGG pathways
MAP codePathways
MAP00010Glycolysis / Gluconeogenesis
MAP00020Citrate cycle (TCA cycle)
MAP00620Pyruvate metabolism
MAP00710Carbon fixation in photosynthetic organisms

Swiss-prot:Accession NumberP22259O09460Q6W6X5Q5SLL5P51058
Entry namePPCK_ECOLIPPCK_ANASUQ6W6X5_ACTSCPCKA_THET8PPCK_TRYCR
ActivityATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2).ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2).ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2).ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2).ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2).
SubunitMonomer.


Homodimer (By similarity).
Subcellular locationCytoplasm.Cytoplasm (By similarity).Cytoplasm (By Similarity).Cytoplasm (By similarity).Glycosome (By similarity).
Cofactor






CofactorsSubstratesProductsintermediates
KEGG-idC00305C02148C00002C00036C00008C00074C00011I00001
CompoundMagnesiumDivalent metalATPOxaloacetateADPPhosphoenolpyruvateCO2EnolpyruvateTransition-state of phosphoryl transfer
Typedivalent metal (Ca2+, Mg2+)divalent metal (Ca2+, Mg2+)amine group,nucleotidecarbohydrate,carboxyl groupamine group,nucleotidecarboxyl group,phosphate group/phosphate ionothers

1aq2A01UnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:PYRUnbound
1aylA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:OXLUnbound
1oenA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1k3cA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:PYRUnbound
1k3dA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1os1A01UnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:PYRUnbound
1yvyA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1yvyB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ylhA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:PYRUnbound
1wg9A01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1wg9B01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ii2A01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ii2B01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1aq2A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1aylA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1oenA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1k3cA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1k3dA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1os1A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1yvyA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1yvyB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ylhA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1wg9A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1wg9B02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ii2A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ii2B02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1aq2A03Bound:_MGBound:_MNBound:ATPUnboundUnboundUnboundUnboundUnboundUnbound
1aylA03Bound:_MGUnboundBound:ATPUnboundUnboundUnboundUnboundUnboundUnbound
1oenA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1k3cA03Bound:_MGUnboundUnboundUnboundBound:ADPUnboundUnboundUnboundTransition-state-analogue:ADP-AF3-PYR
1k3dA03Bound:_MGUnboundUnboundUnboundBound:ADPUnboundUnboundUnboundTransition-state-analogue:ADP-AF3
1os1A03Bound:_MGBound:_CABound:ATPUnboundUnboundUnboundUnboundUnboundUnbound
1yvyA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1yvyB03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ylhA03UnboundBound:_MNUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1wg9A03UnboundUnboundBound:ATPUnboundUnboundUnboundUnboundUnboundUnbound
1wg9B03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ii2A03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ii2B03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [3], [4], [7], [13], [20] & [22]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
1aq2A01TYR  207
LYS  213(2nd metal binding)

1aylA01TYR  207
LYS  213(2nd metal binding)

1oenA01TYR  207
LYS  213(2nd metal binding)

1k3cA01TYR  207
LYS  213(2nd metal binding)

1k3dA01TYR  207
LYS  213(2nd metal binding)

1os1A01TYR  207
LYS  213(2nd metal binding)

1yvyA01TYR  200
LYS  206(2nd metal binding)

1yvyB01TYR 1200
LYS 1206(2nd metal binding)

1ylhA01TYR  207
LYS  213(2nd metal binding)

1wg9A01TYR  191
LYS  197(2nd metal binding)

1wg9B01TYR  191
LYS  197(2nd metal binding)

1ii2A01TYR  180
LYS  186(2nd metal binding)

1ii2B01TYR  180
LYS  186(2nd metal binding)

1aq2A02ARG  333


1aylA02ARG  333


1oenA02ARG  333


1k3cA02ARG  333


1k3dA02ARG  333


1os1A02ARG  333


1yvyA02ARG  327


1yvyB02ARG 1327


1ylhA02ARG  333


1wg9A02ARG  319


1wg9B02ARG  319


1ii2A02ARG  307


1ii2B02ARG  307


1aq2A03LYS  254
HIS  232;ASP  269(2nd metal binding);THR  255(Magnesium binding)
GLY  251
1aylA03LYS  254
HIS  232;ASP  269(2nd metal binding);THR  255(Magnesium binding)
GLY  251
1oenA03LYS  254
HIS  232;ASP  269(2nd metal binding);THR  255(Magnesium binding)
GLY  251
1k3cA03LYS  254
HIS  232;ASP  269(2nd metal binding);THR  255(Magnesium binding)
GLY  251
1k3dA03LYS  254
HIS  232;ASP  269(2nd metal binding);THR  255(Magnesium binding)
GLY  251
1os1A03LYS  254
HIS  232;ASP  269(2nd metal binding);THR  255(Magnesium binding)
GLY  251
1yvyA03LYS  248
HIS  225;ASP  263(2nd metal binding);THR  249(Magnesium binding)
GLY  245
1yvyB03LYS 1248
HIS 1225;ASP 1263(2nd metal binding);THR 1249(Magnesium binding)
GLY 1245
1ylhA03LYS  254
HIS  232;ASP  269(2nd metal binding);THR  255(Magnesium binding)
GLY  251
1wg9A03LYS  238
HIS  216;ASP  253(2nd metal binding);THR  239(Magnesium binding)
GLY  235
1wg9B03LYS  238
HIS  216;ASP  253(2nd metal binding);THR  239(Magnesium binding)
GLY  235
1ii2A03LYS  227
HIS  205;ASP  242(2nd metal binding);THR  228(Magnesium binding)
GLY  224
1ii2B03LYS  227
HIS  205;ASP  242(2nd metal binding);THR  228(Magnesium binding)
GLY  224

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]p.133-135
[3]Fig.8, p.360-3612
[5]Scheme 2, p.8107-81082
[6]Fig.3, p.992-9943
[7]p.6300-6301
[9]p.3-5
[11]p.87-89
[12]p.1064-1066
[13]

[14]

[20]Fig.9, p.4240-42413
[22]Fig.4. p.2752
[23]Fig.7, p.1835

references
[1]
PubMed ID7756267
JournalBiochemistry
Year1995
Volume34
Pages6382-8
AuthorsKrautwurst H, Encinas MV, Marcus F, Latshaw SP, Kemp RG, Frey PA, Cardemil E
TitleSaccharomyces cerevisiae phosphoenolpyruvate carboxykinase: revised amino acid sequence, site-directed mutagenesis, and microenvironment characteristics of cysteines 365 and 458.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID96190956
PubMed ID8609605
JournalJ Mol Biol
Year1996
Volume256
Pages126-43
AuthorsMatte A, Goldie H, Sweet RM, Delbaere LT
TitleCrystal structure of Escherichia coli phosphoenolpyruvate carboxykinase: a new structural family with the P-loop nucleoside triphosphate hydrolase fold.
Related PDB1oen
Related Swiss-protP22259
[3]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID96185447
PubMed ID8599762
JournalNat Struct Biol
Year1996
Volume3
Pages355-63
AuthorsTari LW, Matte A, Pugazhenthi U, Goldie H, Delbaere LT
TitleSnapshot of an enzyme reaction intermediate in the structure of the ATP-Mg2+-oxalate ternary complex of Escherichia coli PEP carboxykinase.
Related PDB1ayl
Related Swiss-protP22259
[4]
PubMed ID9048893
JournalBiochim Biophys Acta
Year1997
Volume1337
Pages166-74
AuthorsBazaes S, Montecinos L, Krautwurst H, Goldie H, Cardemil E, Jabalquinto AM
TitleIdentification of reactive conserved histidines in phosphoenolpyruvate carboxykinases from Escherichia coli and Saccharomyces cerevisiae.
[5]
PubMed ID9139042
JournalJ Biol Chem
Year1997
Volume272
Pages8105-8
AuthorsMatte A, Tari LW, Goldie H, Delbaere LT
TitleStructure and mechanism of phosphoenolpyruvate carboxykinase.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID98069645
PubMed ID9406547
JournalNat Struct Biol
Year1997
Volume4
Pages990-4
AuthorsTari LW, Matte A, Goldie H, Delbaere LT
TitleMg(2+)-Mn2+ clusters in enzyme-catalyzed phosphoryl-transfer reactions.
Related PDB1aq2
Related Swiss-protP22259
[7]
PubMed ID9572844
JournalBiochemistry
Year1998
Volume37
Pages6295-302
AuthorsKrautwurst H, Bazaes S, Gonzalez FD, Jabalquinto AM, Frey PA, Cardemil E
TitleThe strongly conserved lysine 256 of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase is essential for phosphoryl transfer.
[8]
PubMed ID10609641
JournalJ Protein Chem
Year1999
Volume18
Pages659-64
AuthorsJabalquinto AM, Laivenieks M, Zeikus JG, Cardemil E
TitleCharacterization of the oxaloacetate decarboxylase and pyruvate kinase-like activities of Saccharomyces cerevisiae and Anaerobiospirillum succiniciproducens phosphoenolpyruvate carboxykinases.
[9]
PubMed ID11277994
JournalFEBS Lett
Year2001
Volume493
Pages1-5
AuthorsLlanos L, Briones R, Yevenes A, Gonzalez-Nilo FD, Frey PA, Cardemil E
TitleMutation Arg336 to Lys in Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase originates an enzyme with increased oxaloacetate decarboxylase activity.
[10]
PubMed ID11445561
JournalJ Biol Chem
Year2001
Volume276
Pages33705-10
AuthorsYeagley D, Guo S, Unterman T, Quinn PG
TitleGene- and activation-specific mechanisms for insulin inhibition of basal and glucocorticoid-induced insulin-like growth factor binding protein-1 and phosphoenolpyruvate carboxykinase transcription. Roles of forkhead and insulin response sequences.
[11]
PubMed ID11724534
JournalJ Mol Biol
Year2001
Volume314
Pages83-92
AuthorsSudom AM, Prasad L, Goldie H, Delbaere LT
TitleThe phosphoryl-transfer mechanism of Escherichia coli phosphoenolpyruvate carboxykinase from the use of AlF(3).
Related PDB1k3c,1k3d
[12]
PubMed ID11700062
JournalJ Mol Biol
Year2001
Volume313
Pages1059-72
AuthorsTrapani S, Linss J, Goldenberg S, Fischer H, Craievich AF, Oliva G
TitleCrystal structure of the dimeric phosphoenolpyruvate carboxykinase (PEPCK) from Trypanosoma cruzi at 2 A resolution.
Related PDB1ii2
[13]
PubMed ID12379119
JournalBiochemistry
Year2002
Volume41
Pages12763-70
AuthorsKrautwurst H, Roschzttardtz H, Bazaes S, Gonzalez-Nilo FD, Nowak T, Cardemil E
TitleLysine 213 and histidine 233 participate in Mn(II) binding and catalysis in Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase.
[14]
PubMed ID12479406
JournalBiochim Biophys Acta
Year2002
Volume1599
Pages65-71
AuthorsGonzalez-Nilo FD, Krautwurst H, Yevenes A, Cardemil E, Cachau R
TitleSaccharomyces cerevisiae phosphoenolpyruvate carboxykinase: theoretical and experimental study of the effect of glutamic acid 284 on the protonation state of lysine 213.
[15]
PubMed ID12062398
JournalFEBS Lett
Year2002
Volume517
Pages1-6
AuthorsRussell RB, Marquez JA, Hengstenberg W, Scheffzek K
TitleEvolutionary relationship between the bacterial HPr kinase and the ubiquitous PEP-carboxykinase: expanding the P-loop nucleotidyl transferase superfamily.
[16]
PubMed ID11943595
JournalInt J Biochem Cell Biol
Year2002
Volume34
Pages645-56
AuthorsEncinas MV, Gonzalez-Nilo FD, Andreu JM, Alfonso C, Cardemil E
TitleUrea-induced unfolding studies of free- and ligand-bound tetrameric ATP-dependent Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase. Influence of quaternary structure on protein conformational stability.
[17]
PubMed ID11851336
JournalJ Mol Biol
Year2002
Volume316
Pages257-64
AuthorsDunten P, Belunis C, Crowther R, Hollfelder K, Kammlott U, Levin W, Michel H, Ramsey GB, Swain A, Weber D, Wertheimer SJ
TitleCrystal structure of human cytosolic phosphoenolpyruvate carboxykinase reveals a new GTP-binding site.
[18]
PubMed ID12523647
JournalJ Protein Chem
Year2002
Volume21
Pages443-5
AuthorsJabalquinto AM, Laivenieks M, Cabezas M, Zeikus JG, Cardemil E
TitleThe effect of active site mutations in the oxaloacetate decarboxylase and pyruvate kinase-like activities of Anaerobiospirillum succiniciproducens phosphoenolpyruvate carboxykinase.
[19]
PubMed ID12359875
JournalProc Natl Acad Sci U S A
Year2002
Volume99
Pages13437-41
AuthorsFieulaine S, Morera S, Poncet S, Mijakovic I, Galinier A, Janin J, Deutscher J, Nessler S
TitleX-ray structure of a bifunctional protein kinase in complex with its protein substrate HPr.
[20]
PubMed ID12837799
JournalJ Bacteriol
Year2003
Volume185
Pages4233-42
AuthorsSudom A, Walters R, Pastushok L, Goldie D, Prasad L, Delbaere LT, Goldie H
TitleMechanisms of activation of phosphoenolpyruvate carboxykinase from Escherichia coli by Ca2+ and of desensitization by trypsin.
Related PDB1os1
[21]
PubMed ID13678294
JournalJ Protein Chem
Year2003
Volume22
Pages311-5
AuthorsRavanal MC, Goldie H, Cardemil E
TitleThermal stability of phosphoenolpyruvate carboxykinases from Escherichia coli, Trypanosoma brucei, and Saccharomyces cerevisiae.
[22]
PubMed ID15023367
JournalBiochim Biophys Acta
Year2004
Volume1697
Pages271-8
AuthorsDelbaere LT, Sudom AM, Prasad L, Leduc Y, Goldie H
TitleStructure/function studies of phosphoryl transfer by phosphoenolpyruvate carboxykinase.
[23]
PubMed ID15890557
JournalInt J Biochem Cell Biol
Year2005
Volume37
Pages1829-37
AuthorsCotelesage JJ, Prasad L, Zeikus JG, Laivenieks M, Delbaere LT
TitleCrystal structure of Anaerobiospirillum succiniciproducens PEP carboxykinase reveals an important active site loop.
Related PDB1yvy
[24]
PubMed ID15983413
JournalActa Crystallogr D Biol Crystallogr
Year2005
Volume61
Pages903-12
AuthorsLeduc YA, Prasad L, Laivenieks M, Zeikus JG, Delbaere LT
TitleStructure of PEP carboxykinase from the succinate-producing Actinobacillus succinogenes: a new conserved active-site motif.
Related PDB1ylh

comments
There are several types of Phosphoenolpyruvate carboxykinases;
E.C. 4.1.1.49 (ATP-dependent and found in plants and microorganisms),
E.C. 4.1.1.32 (GTP-dependent and found in higher organism),
and E.C. 4.1.1.38 (diphosphate-dependent).
This enzyme belongs to the ATP-dependent one.
Interestingly, lysine residue is coordinated to the divalent metal ion, as it is deprotonated (see [13] & [14]). This enzyme binds a magnesium ion, which is bound to beta- and gamma-phosphate groups of ATP, and a second divalent metal, which is bound between ATP and another substrate. Both the metal ions are involved in catalysis.
According to the literature [3], [5], [6], [7], [11], [20] & [22], this enzyme catalyzes two successive reactions, (A) decarboxylation and (B) phophoryl transfer as follows;
(A) Decarboxylation; Eliminative double-bond formation.
(A1) A divalent metal ion such as manganese and calcium facilitates the bond cleavage between the mehtylene carbon and carboxylate (probably through a water). On the other hand, the leaving carboxylate group is stabilized by Tyr207 (of 2aq2).
(A2) Bond cleavage occurs via E1-like mechanism, forming an enolpyruvate intermediate.
(B) Transfer of phosphoryl group from ATP to enolepyruvate intermediate (see [6], [20] & [22]).
(B1) In the initial stage, a divalent metal is bound to gamma-phosphate and two water, along with Asp269/His232/Lys213 (in the case of manganese). The oxygen of the enolate intermediate is away from the divalent metal ion (in the case of manganese).
(B2) The magnesium ion, bound to the beta- and gamma-phosphate oxygens, stabilizes the negative charge developed on the leaving phosphate and transferred phosphate together with the sidechain of Lys254 and the mainchain amide of Gly251, and polarizes the P-O bond in the gamma-phosphoryl group by making the gamma-phosphate more electrophilic.
(B3) (In the case of manganese ion as the second metal ion, the enol oxygen displaces a water molecule bound to the divalent metal, in order to be in line with the gamma-phosphate group.)
(B4) The second metal ion neutralizes the electrostatic repulsion between the enol oxygen and phosphate group, along with Arg333.
(B5) The enol oxygen makes a nucleophilic attack on the gamma-phosphorus atom. The transfer reaction occurs via SN-2-like mechanism.

createdupdated
2004-07-072009-04-03


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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