EzCatDB: T00217
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeT00217
RLCP classification3.110.90030.330 : Transfer
5.305.2200100.675 : Elimination
CATH domainDomain 11.20.1100.10Catalytic domain
Domain 23.20.20.60 : TIM BarrelCatalytic domain
Domain 31.-.-.-
E.C.4.1.1.31
CSA1jqn,1qb4

CATH domainRelated DB codes (homologues)
3.20.20.60 : TIM BarrelS00241,S00197,S00242,T00043,D00477

Enzyme Name
UniProtKBKEGG

P00864P04711
Protein namePhosphoenolpyruvate carboxylasePhosphoenolpyruvate carboxylase 1phosphoenolpyruvate carboxylase
phosphopyruvate (phosphate) carboxylase
PEP carboxylase
phosphoenolpyruvic carboxylase
PEPC
PEPCase
phosphate:oxaloacetate carboxy-lyase (phosphorylating)
SynonymsPEPCase
PEPC
EC 4.1.1.31
PEPCase 1
PEPC 1
EC 4.1.1.31
RefSeqNP_418391.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491496.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_001105418.1 (Protein)
NM_001111948.1 (DNA/RNA sequence)
PfamPF00311 (PEPcase)
[Graphical view]
PF00311 (PEPcase)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00620Pyruvate metabolism
MAP00710Carbon fixation in photosynthetic organisms
MAP00720Reductive carboxylate cycle (CO2 fixation)

UniProtKB:Accession NumberP00864P04711
Entry nameCAPP_ECOLICAPP1_MAIZE
ActivityPhosphate + oxaloacetate = H(2)O + phosphoenolpyruvate + CO(2).Phosphate + oxaloacetate = H(2)O + phosphoenolpyruvate + CO(2).
SubunitHomotetramer.Homotetramer.
Subcellular location
Cytoplasm.
Cofactor


Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC02148C00074C00011C00001C00009C00036
CompoundDivalent metalPhosphoenolpyruvateCO2H2OOrthophosphateOxaloacetate
Typedivalent metal (Ca2+, Mg2+)carboxyl group,phosphate group/phosphate ionothersH2Ophosphate group/phosphate ioncarbohydrate,carboxyl group
ChEBI
44897
16526
15377
26078
30744
PubChem
59658623
58114173
1005
280
962
22247451
22486802
1004
970
              
1fiyA01UnboundUnboundUnbound UnboundAnalogue:ASP
1jqnA01UnboundUnboundUnbound UnboundAnalogue:ASP
1qb4A01UnboundUnboundUnbound UnboundAnalogue:ASP
1jqoA01UnboundUnboundUnbound Analogue:SO4Unbound
1jqoB01UnboundUnboundUnbound Analogue:SO4Unbound
1fiyA02UnboundUnboundUnbound UnboundUnbound
1jqnA02Bound:_MNAnalogue:DCOUnbound UnboundUnbound
1qb4A02Bound:_MNUnboundUnbound UnboundUnbound
1jqoA02UnboundUnboundUnbound UnboundUnbound
1jqoB02UnboundUnboundUnbound UnboundUnbound
1fiyA03UnboundUnboundUnbound UnboundUnbound
1jqnA03UnboundUnboundUnbound UnboundUnbound
1qb4A03UnboundUnboundUnbound UnboundUnbound
1jqoA03UnboundUnboundUnbound UnboundUnbound
1jqoB03UnboundUnboundUnbound UnboundUnbound

Active-site residues
resource
literature [27] & [28]
pdbCatalytic residuesCofactor-binding residues
          
1fiyA01ARG 699;ARG 713
 
1jqnA01ARG 699;ARG 713
 
1qb4A01ARG 699;ARG 713
 
1jqoA01ARG 759;ARG 773
 
1jqoB01ARG 759;ARG 773
 
1fiyA02HIS 138;ARG 396;ARG 587
GLU 506;ASP 543(Divalent metal binding)
1jqnA02HIS 138;ARG 396;ARG 587
GLU 506;ASP 543(Divalent metal binding)
1qb4A02HIS 138;ARG 396;ARG 587
GLU 506;ASP 543(Divalent metal binding)
1jqoA02HIS 177;ARG 456;ARG 647
GLU 566;ASP 603(Divalent metal binding)
1jqoB02HIS 177;ARG 456;ARG 647
GLU 566;ASP 603(Divalent metal binding)
1fiyA03 
 
1jqnA03 
 
1qb4A03 
 
1jqoA03 
 
1jqoB03 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]SCHEME 22
[4]Fig.9, p.3453463
[11]Scheme 2
[14]Scheme 12
[16]Fig.3
[17]Fig.5
[24]Fig.3B, p.963
[27]Fig.5, p.1725-17285
[28]Fig.4, p.1765

references
[1]
PubMed ID7174666
JournalJ Biol Chem
Year1982
Volume257
Pages14795-8
AuthorsHansen DE, Knowles JR
TitleThe stereochemical course at phosphorus of the reaction catalyzed by phosphoenolpyruvate carboxylase.
[2]
PubMed ID4014670
JournalAnal Biochem
Year1985
Volume145
Pages393-7
AuthorsHatch MD, Heldt HW
TitleSynthesis, storage, and stability of [4-14C]oxaloacetic acid.
[3]
PubMed ID3085590
JournalArch Biochem Biophys
Year1986
Volume246
Pages546-53
AuthorsPodesta FE, Iglesias AA, Andreo CS
TitleModification of an essential amino group of phosphoenolpyruvate carboxylase from maize leaves by pyridoxal phosphate and by pyridoxal phosphate-sensitized photooxidation.
[4]
PubMed ID3091111
JournalBiosci Rep
Year1986
Volume6
Pages335-47
AuthorsRubio V
TitleEnzymatic HCO3- fixation: a common mechanism for all enzymes involved?
[5]
PubMed ID3519602
JournalJ Biochem (Tokyo)
Year1986
Volume99
Pages1299-310
AuthorsIshijima S, Izui K, Katsuki H
TitlePhosphoenolpyruvate carboxylase of Escherichia coli K-12. N- and C-terminal sequences and tentative assignment of the catalytically essential cysteine residue.
[6]
PubMed ID3111298
JournalAnal Biochem
Year1987
Volume162
Pages358-62
AuthorsO'Leary MH, Hermes JD
TitleDetermination of substrate specificity of carboxylases by nuclear magnetic resonance.
[7]
PubMed ID3569281
JournalEur J Biochem
Year1987
Volume164
Pages661-6
AuthorsWagner R, Gonzalez DH, Podesta FE, Andreo CS
TitleChanges in the quaternary structure of phosphoenolpyruvate carboxylase induced by ionic strength affect its catalytic activity.
[8]
PubMed ID3240340
JournalBiochemistry
Year1988
Volume27
Pages1342-7
AuthorsSikkema KD, O'Leary MH
TitleSynthesis and study of phosphoenolthiopyruvate.
[9]
PubMed ID3365391
JournalBiochemistry
Year1988
Volume27
Pages1355-60
AuthorsWirsching P, O'Leary MH
Title1-Carboxyallenyl phosphate, an allenic analogue of phosphoenolpyruvate.
[10]
PubMed ID3365390
JournalBiochemistry
Year1988
Volume27
Pages1348-55
AuthorsWirsching P, O'Leary MH
Title(Z)-3-(fluoromethyl)phosphoenolpyruvate: synthesis and enzymatic studies.
[11]
PubMed ID3360012
JournalEur J Biochem
Year1988
Volume173
Pages339-43
AuthorsGonzalez DH, Andreo CS
TitleStereoselectivity of the interaction of E- and Z-2-phosphoenolbutyrate with maize leaf phosphoenolpyruvate carboxylase.
[12]
PubMed ID2453360
JournalEur J Biochem
Year1988
Volume173
Pages561-8
AuthorsWagner R, Podesta FE, Gonzalez DH, Andreo CS
TitleProximity between fluorescent probes attached to four essential lysyl residues in phosphoenolpyruvate carboxylase. A resonance energy transfer study.
[13]
CommentsCRYSTALLIZATION.
Medline ID90012219
PubMed ID2677392
JournalJ Mol Biol
Year1989
Volume208
Pages509-10
AuthorsInoue M, Hayashi M, Sugimoto M, Harada S, Kai Y, Kasai N, Terada K, Izui K
TitleFirst crystallization of a phosphoenolpyruvate carboxylase from Escherichia coli.
Related UniProtKBP00864
[14]
CommentsMUTAGENESIS OF HIS-138.
Medline ID92111527
PubMed ID1765093
JournalEur J Biochem
Year1991
Volume202
Pages797-803
AuthorsTerada K, Izui K
TitleSite-directed mutagenesis of the conserved histidine residue of phosphoenolpyruvate carboxylase. His138 is essential for the second partial reaction.
Related UniProtKBP00864
[15]
CommentsMUTAGENESIS OF HIS-579.
Medline ID91201285
PubMed ID2016273
JournalJ Biochem (Tokyo)
Year1991
Volume109
Pages49-54
AuthorsTerada K, Murata T, Izui K
TitleSite-directed mutagenesis of phosphoenolpyruvate carboxylase from E. coli: the role of His579 in the catalytic and regulatory functions.
Related UniProtKBP00864
[16]
PubMed ID1321659
JournalBiochemistry
Year1992
Volume31
Pages6441-6
AuthorsJanc JW, Cleland WW, O'Leary MH
TitleMechanistic studies of phosphoenolpyruvate carboxylase from Zea mays utilizing formate as an alternate substrate for bicarbonate.
[17]
PubMed ID1633157
JournalBiochemistry
Year1992
Volume31
Pages6432-40
AuthorsJanc JW, Urbauer JL, O'Leary MH, Cleland WW
TitleMechanistic studies of phosphoenolpyruvate carboxylase from Zea mays with (Z)- and (E)-3-fluorophosphoenolpyruvate as substrates.
[18]
PubMed ID7851427
JournalEur J Biochem
Year1995
Volume227
Pages488-93
AuthorsRollin C, Morgant V, Guyonvarch A, Guerquin-Kern JL
Title13C-NMR studies of Corynebacterium melassecola metabolic pathways.
[19]
CommentsMUTAGENESIS OF ARG-587.
Medline ID96104989
PubMed ID7490260
JournalJ Biochem (Tokyo)
Year1995
Volume117
Pages1196-200
AuthorsYano M, Terada K, Umiji K, Izui K
TitleCatalytic role of an arginine residue in the highly conserved and unique sequence of phosphoenolpyruvate carboxylase.
Related UniProtKBP00864
[20]
PubMed ID7768910
JournalJ Biol Chem
Year1995
Volume270
Pages13147-59
AuthorsDieuaide-Noubhani M, Raffard G, Canioni P, Pradet A, Raymond P
TitleQuantification of compartmented metabolic fluxes in maize root tips using isotope distribution from 13C- or 14C-labeled glucose.
[21]
PubMed ID9095558
JournalBiosci Biotechnol Biochem
Year1997
Volume61
Pages545-6
AuthorsDong LY, Hata S, Izui K
TitleHigh-level expression of maize C4-type phosphoenolpyruvate carboxylase in Escherichia coli and its rapid purification.
[22]
PubMed ID9522466
JournalPlant Cell Physiol
Year1997
Volume38
Pages1340-5
AuthorsDong LY, Ueno Y, Hata S, Izui K
TitleEffects of site-directed mutagenesis of conserved Lys606 residue on catalytic and regulatory functions of maize C4-form phosphoenolpyruvate carboxylase.
[23]
PubMed ID10525297
JournalArch Biochem Biophys
Year1999
Volume371
Pages124-8
AuthorsDong L, Patil S, Condon SA, Haas EJ, Chollet R
TitleThe conserved C-terminal tetrapeptide of sorghum C(4) phosphoenolpyruvate carboxylase is indispensable for maximal catalytic activity, but not for homotetramer formation.
[24]
PubMed ID10481043
JournalFEBS Lett
Year1999
Volume458
Pages93-6
AuthorsMatsumura H, Terada M, Shirakata S, Inoue T, Yoshinaga T, Izui K, Kai Y
TitlePlausible phosphoenolpyruvate binding site revealed by 2.6 A structure of Mn2+-bound phosphoenolpyruvate carboxylase from Escherichia coli.
Related PDB1qb4
[25]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
Medline ID99128321
PubMed ID9927652
JournalProc Natl Acad Sci U S A
Year1999
Volume96
Pages823-8
AuthorsKai Y, Matsumura H, Inoue T, Terada K, Nagara Y, Yoshinaga T, Kihara A, Tsumura K, Izui K
TitleThree-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition.
Related PDB1fiy
Related UniProtKBP00864
[26]
PubMed ID12366798
JournalPlant J
Year2002
Volume32
Pages25-39
AuthorsRademacher T, Hausler RE, Hirsch HJ, Zhang L, Lipka V, Weier D, Kreuzaler F, Peterhansel C
TitleAn engineered phosphoenolpyruvate carboxylase redirects carbon and nitrogen flow in transgenic potato plants.
[27]
PubMed ID12467579
JournalStructure (Camb)
Year2002
Volume10
Pages1721-30
AuthorsMatsumura H, Xie Y, Shirakata S, Inoue T, Yoshinaga T, Ueno Y, Izui K, Kai Y
TitleCrystal structures of C4 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases.
Related PDB1jqn,1jqo
[28]
PubMed ID12781768
JournalArch Biochem Biophys
Year2003
Volume414
Pages170-9
AuthorsKai Y, Matsumura H, Izui K
TitlePhosphoenolpyruvate carboxylase: three-dimensional structure and molecular mechanisms.
[29]
PubMed ID12781769
JournalArch Biochem Biophys
Year2003
Volume414
Pages180-8
AuthorsSvensson P, Blasing OE, Westhoff P
TitleEvolution of C4 phosphoenolpyruvate carboxylase.
[30]
PubMed ID12805637
JournalPlant Physiol
Year2003
Volume132
Pages1097-106
AuthorsAlvarez R, Garcia-Maurino S, Feria AB, Vidal J, Echevarria C
TitleA 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.

comments
According to the literature [27] & [28], this enzyme catalyzes the following reactions:
(A) Transfer of phosphate from phosphoenolpyruvate (PEP) to oxygen atom of bicarbonate(CO2 + H2O = H2CO3);
(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.

createdupdated
2004-07-152009-02-26
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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.