EzCatDB: D00111

DB codeD00111
RLCP classification3.103.69900.359
CATH domainDomain 13.40.50.450Catalytic domain
Domain 23.40.50.460Catalytic domain
E.C.2.7.1.11
CSA1pfk


Enzyme Name
Swiss-protKEGG

P00512P0A796
Protein name6-phosphofructokinase6-phosphofructokinase isozyme 16-phosphofructokinase
phosphohexokinase
phosphofructokinase I
phosphofructokinase (phosphorylating)
6-phosphofructose 1-kinase
ATP-dependent phosphofructokinase
D-fructose-6-phosphate 1-phosphotransferase
fructose 6-phosphate kinase
fructose 6-phosphokinase
nucleotide triphosphate-dependent phosphofructokinase
phospho-1,6-fructokinase
PFK
SynonymsPhosphofructokinase
EC 2.7.1.11
Phosphohexokinase
EC 2.7.1.11
6-phosphofructokinase isozyme I
Phosphofructokinase 1
Phosphohexokinase 1

KEGG pathways
MAP codePathways
MAP00010Glycolysis / Gluconeogenesis
MAP00030Pentose phosphate pathway
MAP00051Fructose and mannose metabolism
MAP00052Galactose metabolism

Swiss-prot:Accession NumberP00512P0A796
Entry nameK6PF_BACSTK6PF1_ECOLI
ActivityATP + D-fructose 6-phosphate = ADP + D- fructose 1,6-bisphosphate.ATP + D-fructose 6-phosphate = ADP + D- fructose 1,6-bisphosphate.
SubunitHomotetramer.Homotetramer.
Subcellular locationCytoplasm.Cytoplasm.
Cofactor



CofactorsSubstratesProducts
KEGG-idC00305C00002C00085C00008C00354
CompoundMagnesiumATPD-Fructose 6-phosphateADPD-Fructose 1,6-bisphosphate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidecarbohydrate,phosphate group/phosphate ionamine group,nucleotidecarbohydrate,phosphate group/phosphate ion
1pfkA01Bound:_MG 325UnboundUnboundBound:ADP 324Bound:FBP
1pfkB01Bound:_MG 325UnboundUnboundBound:ADP 324Bound:FBP
2pfkA01UnboundUnboundUnboundUnboundUnbound
2pfkB01UnboundUnboundUnboundUnboundUnbound
2pfkC01UnboundUnboundUnboundUnboundUnbound
2pfkD01UnboundUnboundUnboundUnboundUnbound
3pfkA01UnboundUnboundUnboundUnboundUnbound
4pfkA01Bound:_MG 325UnboundBound:F6PBound:ADP 324Unbound
6pfkA01UnboundUnboundUnboundUnboundUnbound
6pfkB01UnboundUnboundUnboundUnboundUnbound
6pfkC01UnboundUnboundUnboundUnboundUnbound
6pfkD01UnboundUnboundUnboundUnboundUnbound
1mtoA01UnboundUnboundBound:F6PUnboundUnbound
1mtoB01UnboundUnboundBound:F6PUnboundUnbound
1mtoC01UnboundUnboundBound:F6PUnboundUnbound
1mtoD01UnboundUnboundBound:F6PUnboundUnbound
1mtoE01UnboundUnboundBound:F6PUnboundUnbound
1mtoF01UnboundUnboundBound:F6PUnboundUnbound
1mtoG01UnboundUnboundBound:F6PUnboundUnbound
1mtoH01UnboundUnboundBound:F6PUnboundUnbound
1pfkA02UnboundUnboundUnboundUnboundBound:FBP
1pfkB02UnboundUnboundUnboundUnboundBound:FBP
2pfkA02UnboundUnboundUnboundUnboundUnbound
2pfkB02UnboundUnboundUnboundUnboundUnbound
2pfkC02UnboundUnboundUnboundUnboundUnbound
2pfkD02UnboundUnboundUnboundUnboundUnbound
3pfkA02UnboundUnboundUnboundUnboundUnbound
4pfkA02UnboundUnboundUnboundUnboundUnbound
6pfkA02UnboundUnboundUnboundUnboundUnbound
6pfkB02UnboundUnboundUnboundUnboundUnbound
6pfkC02UnboundUnboundUnboundUnboundUnbound
6pfkD02UnboundUnboundUnboundUnboundUnbound
1mtoA02UnboundUnboundUnboundUnboundUnbound
1mtoB02UnboundUnboundUnboundUnboundUnbound
1mtoC02UnboundUnboundUnboundUnboundUnbound
1mtoD02UnboundUnboundUnboundUnboundUnbound
1mtoE02UnboundUnboundUnboundUnboundUnbound
1mtoF02UnboundUnboundUnboundUnboundUnbound
1mtoG02UnboundUnboundUnboundUnboundUnbound
1mtoH02UnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot & literature [7] & [11]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
1pfkA01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
1pfkB01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
2pfkA01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
2pfkB01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
2pfkC01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
2pfkD01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
3pfkA01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
4pfkA01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
6pfkA01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
6pfkB01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
6pfkC01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
6pfkD01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
1mtoA01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
1mtoB01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
1mtoC01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
1mtoD01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
1mtoE01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
1mtoF01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
1mtoG01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
1mtoH01ARG 72;THR 125;ASP 127;ASP 129
ASP 103;ASP 129(Magnesium binding)
GLY 11
1pfkA02ARG 171


1pfkB02ARG 171


2pfkA02ARG 171


2pfkB02ARG 171


2pfkC02ARG 171


2pfkD02ARG 171


3pfkA02ARG 171


4pfkA02ARG 171


6pfkA02ARG 171


6pfkB02ARG 171


6pfkC02ARG 171


6pfkD02ARG 171


1mtoA02ARG 171


1mtoB02ARG 171


1mtoC02ARG 171


1mtoD02ARG 171


1mtoE02ARG 171


1mtoF02ARG 171


1mtoG02ARG 171


1mtoH02ARG 171



References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.58-60
[7]p.984-986, p.992
[10]

[11]


references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
Medline ID79199719
PubMed ID156307
JournalNature
Year1979
Volume279
Pages500-4
AuthorsEvans PR, Hudson PJ
TitleStructure and control of phosphofructokinase from Bacillus stearothermophilus.
Related Swiss-protP00512
[2]
PubMed ID6462132
JournalBiochem J
Year1981
Volume199
Pages427-32
AuthorsJarvest RL, Lowe G, Potter BV
TitleThe stereochemical course of phosphoryl transfer catalysed by Bacillus stearothermophilus and rabbit skeletal-muscle phosphofructokinase with a chiral [16O,17O,18O]phosphate ester.
[3]
CommentsX-ray crystallography
PubMed ID6115424
JournalPhilos Trans R Soc Lond B Biol Sci
Year1981
Volume293
Pages53-62
AuthorsEvans PR, Farrants GW, Hudson PJ
TitlePhosphofructokinase: structure and control.
Related PDB3pfk,4pfk
[4]
PubMed ID6115426
JournalPhilos Trans R Soc Lond B Biol Sci
Year1981
Volume293
Pages75-92
AuthorsLowe G, Cullis PM, Jarvest RL, Potter BV, Sproat BS
TitleStereochemistry of phosphoryl transfer.
[5]
PubMed ID2949086
JournalJ Mol Biol
Year1986
Volume191
Pages713-20
AuthorsEvans PR, Farrants GW, Lawrence MC
TitleCrystallographic structure of allosterically inhibited phosphofructokinase at 7 A resolution.
[6]
PubMed ID2952886
JournalNature
Year1987
Volume326
Pages811-2
AuthorsLau FT, Fersht AR
TitleConversion of allosteric inhibition to activation in phosphofructokinase by protein engineering.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
Medline ID89125622
PubMed ID2975709
JournalJ Mol Biol
Year1988
Volume204
Pages973-94
AuthorsShirakihara Y, Evans PR
TitleCrystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction products.
Related PDB1pfk
Related Swiss-protP0A796
[8]
CommentsX-ray crystallography
PubMed ID2527305
JournalJ Mol Biol
Year1989
Volume207
Pages805-21
AuthorsRypniewski WR, Evans PR
TitleCrystal structure of unliganded phosphofructokinase from Escherichia coli.
Related PDB2pfk
[9]
CommentsX-ray crystallography
PubMed ID2136935
JournalNature
Year1990
Volume343
Pages140-5
AuthorsSchirmer T, Evans PR
TitleStructural basis of the allosteric behaviour of phosphofructokinase.
Related PDB6pfk
[10]
PubMed ID1386803
JournalEur J Biochem
Year1992
Volume207
Pages1109-14
AuthorsLaine R, Deville-Bonne D, Auzat I, Garel JR
TitleInteraction between the carboxyl groups of Asp127 and Asp129 in the active site of Escherichia coli phosphofructokinase.
[11]
PubMed ID1304907
JournalProtein Sci
Year1992
Volume1
Pages254-8
AuthorsAuzat I, Garel JR
TitlepH dependence of the reverse reaction catalyzed by phosphofructokinase I from Escherichia coli: implications for the role of Asp 127.
[12]
PubMed ID7876126
JournalJ Biol Chem
Year1995
Volume270
Pages3828-35
AuthorsByrnes WM, Hu W, Younathan ES, Chang SH
TitleA chimeric bacterial phosphofructokinase exhibits cooperativity in the absence of heterotropic regulation.
[13]
PubMed ID7783204
JournalJ Mol Biol
Year1995
Volume249
Pages478-92
AuthorsAuzat I, Gawlita E, Garel JR
TitleSlow ligand-induced transitions in the allosteric phosphofructokinase from Escherichia coli.
[14]
PubMed ID7869376
JournalJ Mol Biol
Year1995
Volume246
Pages248-53
AuthorsAuzat I, Le Bras G, Garel JR
TitleHypercooperativity induced by interface mutations in the phosphofructokinase from Escherichia coli.
[15]
PubMed ID11976749
JournalArch Microbiol
Year2002
Volume177
Pages401-9
AuthorsHansen T, Musfeldt M, Schonheit P
TitleATP-dependent 6-phosphofructokinase from the hyperthermophilic bacterium Thermotoga maritima: characterization of an extremely thermophilic, allosterically regulated enzyme.
[16]
PubMed ID12390023
JournalBiochemistry
Year2002
Volume41
Pages12967-74
AuthorsRiley-Lovingshimer MR, Ronning DR, Sacchettini JC, Reinhart GD
TitleReversible ligand-induced dissociation of a tryptophan-shift mutant of phosphofructokinase from Bacillus stearothermophilus.
Related PDB1mto

comments
This enzyme contains two binding sites for ADP-Mg2+; one is the active site between the two domains, and the other is effector site in the smaller subunit. Moreover, this enzyme has two conformational states, R- and T-states, by allosteric behavior (see [9]).
According to the literature [7], [10] & [11], the reaction proceeds as follows:
(1) Asp127 acts as a general base, whose pKa seems to be modulated by Asp129, to deprotonate the acceptor group, 1-OH of Fructose 6-phosphate (F6P). Asp129 is also involved indirectly in binding of the cofactor magnesium ion, through water molecules.
(2) The activated acceptor group makes a nucleophilic attack on the gamma-phosphate of ATP.
(3) The pentacovalent phosphoryl group is stabilized by Arg171, Arg72, Thr125 and mainchain amide of Gly11, along with the magnesium ion bound to Asp103. The magnesium ion bridges gamma- and beta-phosphate groups.

createdupdated
2004-10-152009-02-26
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 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)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.