DB code: T00217

RLCP classification 3.110.90030.330 : Transfer
5.305.2200100.675 : Elimination
CATH domain 1.20.1100.10 : Catalytic domain
3.20.20.60 : TIM Barrel Catalytic domain
1.-.-.- :
E.C. 4.1.1.31
CSA 1qb4 1jqn
M-CSA 1qb4 1jqn
MACiE

CATH domain Related DB codes (homologues)
3.20.20.60 : TIM Barrel S00241 S00197 S00242 T00043 D00477

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P00864 Phosphoenolpyruvate carboxylase
PEPCase
PEPC
EC 4.1.1.31
NP_418391.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491496.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00311 (PEPcase)
[Graphical View]
P04711 Phosphoenolpyruvate carboxylase 1
PEPCase 1
PEPC 1
EC 4.1.1.31
NP_001105418.1 (Protein)
NM_001111948.1 (DNA/RNA sequence)
PF00311 (PEPcase)
[Graphical View]

KEGG enzyme name
phosphoenolpyruvate carboxylase
phosphopyruvate (phosphate) carboxylase
PEP carboxylase
phosphoenolpyruvic carboxylase
PEPC
PEPCase
phosphate:oxaloacetate carboxy-lyase (phosphorylating)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00864 CAPP_ECOLI Phosphate + oxaloacetate = H(2)O + phosphoenolpyruvate + CO(2). Homotetramer.
P04711 CAPP1_MAIZE Phosphate + oxaloacetate = H(2)O + phosphoenolpyruvate + CO(2). Homotetramer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00620 Pyruvate metabolism
MAP00710 Carbon fixation in photosynthetic organisms
MAP00720 Reductive carboxylate cycle (CO2 fixation)

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C02148 C00074 C00011 C00001 C00009 C00036
E.C.
Compound Divalent metal Phosphoenolpyruvate CO2 H2O Orthophosphate Oxaloacetate
Type divalent metal (Ca2+, Mg2+) carboxyl group,phosphate group/phosphate ion others H2O phosphate group/phosphate ion carbohydrate,carboxyl group
ChEBI 44897
16526
15377
26078
30744
PubChem 1005
58114173
59658623
280
22247451
962
1004
22486802
970
1fiyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Analogue:ASP
1jqnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Analogue:ASP
1qb4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Analogue:ASP
1jqoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:SO4 Unbound
1jqoB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:SO4 Unbound
1fiyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1jqnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Analogue:DCO Unbound Unbound Unbound
1qb4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Unbound Unbound Unbound Unbound
1jqoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1jqoB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1fiyA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1jqnA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qb4A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1jqoA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1jqoB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [27] & [28]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1fiyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 699;ARG 713
1jqnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 699;ARG 713
1qb4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 699;ARG 713
1jqoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 759;ARG 773
1jqoB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 759;ARG 773
1fiyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 138;ARG 396;ARG 587 GLU 506;ASP 543(Divalent metal binding)
1jqnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 138;ARG 396;ARG 587 GLU 506;ASP 543(Divalent metal binding)
1qb4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 138;ARG 396;ARG 587 GLU 506;ASP 543(Divalent metal binding)
1jqoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 177;ARG 456;ARG 647 GLU 566;ASP 603(Divalent metal binding)
1jqoB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 177;ARG 456;ARG 647 GLU 566;ASP 603(Divalent metal binding)
1fiyA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1jqnA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qb4A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1jqoA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1jqoB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
SCHEME 2 2
[4]
Fig.9, p.345346 3
[11]
Scheme 2
[14]
Scheme 1 2
[16]
Fig.3
[17]
Fig.5
[24]
Fig.3B, p.96 3
[27]
Fig.5, p.1725-1728 5
[28]
Fig.4, p.176 5

References
[1]
Resource
Comments
Medline ID
PubMed ID 7174666
Journal J Biol Chem
Year 1982
Volume 257
Pages 14795-8
Authors Hansen DE, Knowles JR
Title The stereochemical course at phosphorus of the reaction catalyzed by phosphoenolpyruvate carboxylase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 4014670
Journal Anal Biochem
Year 1985
Volume 145
Pages 393-7
Authors Hatch MD, Heldt HW
Title Synthesis, storage, and stability of [4-14C]oxaloacetic acid.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 3085590
Journal Arch Biochem Biophys
Year 1986
Volume 246
Pages 546-53
Authors Podesta FE, Iglesias AA, Andreo CS
Title Modification of an essential amino group of phosphoenolpyruvate carboxylase from maize leaves by pyridoxal phosphate and by pyridoxal phosphate-sensitized photooxidation.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 3091111
Journal Biosci Rep
Year 1986
Volume 6
Pages 335-47
Authors Rubio V
Title Enzymatic HCO3- fixation: a common mechanism for all enzymes involved?
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 3519602
Journal J Biochem (Tokyo)
Year 1986
Volume 99
Pages 1299-310
Authors Ishijima S, Izui K, Katsuki H
Title Phosphoenolpyruvate carboxylase of Escherichia coli K-12. N- and C-terminal sequences and tentative assignment of the catalytically essential cysteine residue.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 3111298
Journal Anal Biochem
Year 1987
Volume 162
Pages 358-62
Authors O'Leary MH, Hermes JD
Title Determination of substrate specificity of carboxylases by nuclear magnetic resonance.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 3569281
Journal Eur J Biochem
Year 1987
Volume 164
Pages 661-6
Authors Wagner R, Gonzalez DH, Podesta FE, Andreo CS
Title Changes in the quaternary structure of phosphoenolpyruvate carboxylase induced by ionic strength affect its catalytic activity.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 3240340
Journal Biochemistry
Year 1988
Volume 27
Pages 1342-7
Authors Sikkema KD, O'Leary MH
Title Synthesis and study of phosphoenolthiopyruvate.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 3365391
Journal Biochemistry
Year 1988
Volume 27
Pages 1355-60
Authors Wirsching P, O'Leary MH
Title 1-Carboxyallenyl phosphate, an allenic analogue of phosphoenolpyruvate.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 3365390
Journal Biochemistry
Year 1988
Volume 27
Pages 1348-55
Authors Wirsching P, O'Leary MH
Title (Z)-3-(fluoromethyl)phosphoenolpyruvate: synthesis and enzymatic studies.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 3360012
Journal Eur J Biochem
Year 1988
Volume 173
Pages 339-43
Authors Gonzalez DH, Andreo CS
Title Stereoselectivity of the interaction of E- and Z-2-phosphoenolbutyrate with maize leaf phosphoenolpyruvate carboxylase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 2453360
Journal Eur J Biochem
Year 1988
Volume 173
Pages 561-8
Authors Wagner R, Podesta FE, Gonzalez DH, Andreo CS
Title Proximity between fluorescent probes attached to four essential lysyl residues in phosphoenolpyruvate carboxylase. A resonance energy transfer study.
Related PDB
Related UniProtKB
[13]
Resource
Comments CRYSTALLIZATION.
Medline ID 90012219
PubMed ID 2677392
Journal J Mol Biol
Year 1989
Volume 208
Pages 509-10
Authors Inoue M, Hayashi M, Sugimoto M, Harada S, Kai Y, Kasai N, Terada K, Izui K
Title First crystallization of a phosphoenolpyruvate carboxylase from Escherichia coli.
Related PDB
Related UniProtKB P00864
[14]
Resource
Comments MUTAGENESIS OF HIS-138.
Medline ID 92111527
PubMed ID 1765093
Journal Eur J Biochem
Year 1991
Volume 202
Pages 797-803
Authors Terada K, Izui K
Title Site-directed mutagenesis of the conserved histidine residue of phosphoenolpyruvate carboxylase. His138 is essential for the second partial reaction.
Related PDB
Related UniProtKB P00864
[15]
Resource
Comments MUTAGENESIS OF HIS-579.
Medline ID 91201285
PubMed ID 2016273
Journal J Biochem (Tokyo)
Year 1991
Volume 109
Pages 49-54
Authors Terada K, Murata T, Izui K
Title Site-directed mutagenesis of phosphoenolpyruvate carboxylase from E. coli: the role of His579 in the catalytic and regulatory functions.
Related PDB
Related UniProtKB P00864
[16]
Resource
Comments
Medline ID
PubMed ID 1321659
Journal Biochemistry
Year 1992
Volume 31
Pages 6441-6
Authors Janc JW, Cleland WW, O'Leary MH
Title Mechanistic studies of phosphoenolpyruvate carboxylase from Zea mays utilizing formate as an alternate substrate for bicarbonate.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 1633157
Journal Biochemistry
Year 1992
Volume 31
Pages 6432-40
Authors Janc JW, Urbauer JL, O'Leary MH, Cleland WW
Title Mechanistic studies of phosphoenolpyruvate carboxylase from Zea mays with (Z)- and (E)-3-fluorophosphoenolpyruvate as substrates.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 7851427
Journal Eur J Biochem
Year 1995
Volume 227
Pages 488-93
Authors Rollin C, Morgant V, Guyonvarch A, Guerquin-Kern JL
Title 13C-NMR studies of Corynebacterium melassecola metabolic pathways.
Related PDB
Related UniProtKB
[19]
Resource
Comments MUTAGENESIS OF ARG-587.
Medline ID 96104989
PubMed ID 7490260
Journal J Biochem (Tokyo)
Year 1995
Volume 117
Pages 1196-200
Authors Yano M, Terada K, Umiji K, Izui K
Title Catalytic role of an arginine residue in the highly conserved and unique sequence of phosphoenolpyruvate carboxylase.
Related PDB
Related UniProtKB P00864
[20]
Resource
Comments
Medline ID
PubMed ID 7768910
Journal J Biol Chem
Year 1995
Volume 270
Pages 13147-59
Authors Dieuaide-Noubhani M, Raffard G, Canioni P, Pradet A, Raymond P
Title Quantification of compartmented metabolic fluxes in maize root tips using isotope distribution from 13C- or 14C-labeled glucose.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 9095558
Journal Biosci Biotechnol Biochem
Year 1997
Volume 61
Pages 545-6
Authors Dong LY, Hata S, Izui K
Title High-level expression of maize C4-type phosphoenolpyruvate carboxylase in Escherichia coli and its rapid purification.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 9522466
Journal Plant Cell Physiol
Year 1997
Volume 38
Pages 1340-5
Authors Dong LY, Ueno Y, Hata S, Izui K
Title Effects of site-directed mutagenesis of conserved Lys606 residue on catalytic and regulatory functions of maize C4-form phosphoenolpyruvate carboxylase.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 10525297
Journal Arch Biochem Biophys
Year 1999
Volume 371
Pages 124-8
Authors Dong L, Patil S, Condon SA, Haas EJ, Chollet R
Title The conserved C-terminal tetrapeptide of sorghum C(4) phosphoenolpyruvate carboxylase is indispensable for maximal catalytic activity, but not for homotetramer formation.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 10481043
Journal FEBS Lett
Year 1999
Volume 458
Pages 93-6
Authors Matsumura H, Terada M, Shirakata S, Inoue T, Yoshinaga T, Izui K, Kai Y
Title Plausible phosphoenolpyruvate binding site revealed by 2.6 A structure of Mn2+-bound phosphoenolpyruvate carboxylase from Escherichia coli.
Related PDB 1qb4
Related UniProtKB
[25]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
Medline ID 99128321
PubMed ID 9927652
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 823-8
Authors Kai Y, Matsumura H, Inoue T, Terada K, Nagara Y, Yoshinaga T, Kihara A, Tsumura K, Izui K
Title Three-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition.
Related PDB 1fiy
Related UniProtKB P00864
[26]
Resource
Comments
Medline ID
PubMed ID 12366798
Journal Plant J
Year 2002
Volume 32
Pages 25-39
Authors Rademacher T, Hausler RE, Hirsch HJ, Zhang L, Lipka V, Weier D, Kreuzaler F, Peterhansel C
Title An engineered phosphoenolpyruvate carboxylase redirects carbon and nitrogen flow in transgenic potato plants.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 12467579
Journal Structure (Camb)
Year 2002
Volume 10
Pages 1721-30
Authors Matsumura H, Xie Y, Shirakata S, Inoue T, Yoshinaga T, Ueno Y, Izui K, Kai Y
Title Crystal structures of C4 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases.
Related PDB 1jqn 1jqo
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 12781768
Journal Arch Biochem Biophys
Year 2003
Volume 414
Pages 170-9
Authors Kai Y, Matsumura H, Izui K
Title Phosphoenolpyruvate carboxylase: three-dimensional structure and molecular mechanisms.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 12781769
Journal Arch Biochem Biophys
Year 2003
Volume 414
Pages 180-8
Authors Svensson P, Blasing OE, Westhoff P
Title Evolution of C4 phosphoenolpyruvate carboxylase.
Related PDB
Related UniProtKB
[30]
Resource
Comments
Medline ID
PubMed ID 12805637
Journal Plant Physiol
Year 2003
Volume 132
Pages 1097-106
Authors Alvarez R, Garcia-Maurino S, Feria AB, Vidal J, Echevarria C
Title A conserved 19-amino acid synthetic peptide from the carboxy terminus of phosphoenolpyruvate carboxylase inhibits the in vitro phosphorylation of the enzyme by the calcium-independent phosphoenolpyruvate carboxylase kinase.
Related PDB
Related UniProtKB

Comments
(A) Transfer of phosphate from phosphoenolpyruvate (PEP) to oxygen atom of bicarbonate(CO2 + H2O = H2CO3);
According to the literature [27] & [28], this enzyme catalyzes the following reactions:
(B) Decarboxylation: Elimination of carboxyl group from carboxyphosphate intermediate (or elimination of phosphate group from carboxyphosphate intermediate);
(C) Addition of negatively charged sp2 carbon atom of pyruvate to carbon dioxide (CO2);
These reactions proceed as follows:
(A) Transfer of phosphate from PEP to oxygen atom of bicarbonate
(A1) The first substrate PEP is bound to Mg2++/Mn2++, which is bound to the sidechains of Glu566 and Asp603 (of PDB;1jqo). The second substrate, bicarbonate composed of CO2 and H2O, approaches the active site.
(A2) The oxygen atom of bicarbonate makes a nucleophilic attack on the phosphate group of PEP. The negative charge of the transferred phosphate group is stabilized by the interaction with the divalent metal (Mg2+/Mn2+) and the positively charged residues, Arg456, Arg759 & Arg773. The divalent metal also interacts with the leaving pyruvate.
(A3) The nucleophilic reaction gives pyruvate and carboxyphosphate intermediates, which are bound to the divalent metal. The carboxyphosphate intermediate is stabilized by His177.
(B) Decarboxylation, or Elimination of phosphate group from carboxyphosphate intermediate;
(B1) The divalent metal ion stabilizes the phosphate group of the intermediate through the interaction.
(B2) His177 acts as a general base, to deprotonate the carboxyl group, leading to the elimination of the phosphate group, which is stabilized by Arg647. This reaction is also assisted by the hydrophobic pocket, which stabilizes the carboxyl group, or leaving CO2.
(B3) His177 now acts as a general acid to protonate the eliminated phosphate.
(C) Addition of negatively charged sp2 carbon atom of pyruvate to CO2;
(C1) The liberated CO2 moves to another intermediate, pyruvate, which is bound to the divalent metal.
(C2) The negatively charged C-3 atom makes a nucleophilic attack on the carbon atom of CO2, leading to the formation of the final product, oxaloacetate.

Created Updated
2004-07-15 2009-02-26