EzCatDB: S00235

DB codeS00235
RLCP classification8.131.708000.451
4.151.766500.451
5.151.2325000.451
8.113.915300.451
CATH domainDomain 13.20.20.70Catalytic domain
E.C.4.1.2.13
CSA1b57
MACiEM0052

CATH domainRelated DB codes (homologues)
3.20.20.70S00215,S00217,S00218,S00219,S00532,S00198,S00220,S00745,S00537,S00538,S00539,S00826,S00841,S00239,S00240,S00243,S00244,S00199,S00200,S00201,S00221,S00222,S00847,S00224,S00225,S00226,D00014,D00029,M00141,T00015,T00239,D00664,D00665,D00804,D00863,T00089

Enzyme Name
Swiss-protKEGG

P0AB71
Protein nameFructose-bisphosphate aldolase class 2fructose-bisphosphate aldolase
aldolase
fructose-1,6-bisphosphate triosephosphate-lyase
fructose diphosphate aldolase
diphosphofructose aldolase
fructose 1,6-diphosphate aldolase
ketose 1-phosphate aldolase
phosphofructoaldolase
zymohexase
fructoaldolase
fructose 1-phosphate aldolase
fructose 1-monophosphate aldolase
1,6-Diphosphofructose aldolase
SMALDO
D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase
SynonymsFBP aldolase
FBPA
EC 4.1.2.13
Fructose-bisphosphate aldolase class II
Fructose-1,6-bisphosphate aldolase

KEGG pathways
MAP codePathways
MAP00010Glycolysis / Gluconeogenesis
MAP00030Pentose phosphate pathway
MAP00051Fructose and mannose metabolism
MAP00710Carbon fixation in photosynthetic organisms

Swiss-prot:Accession NumberP0AB71
Entry nameALF_ECOLI
ActivityD-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate.
SubunitHomodimer.
Subcellular location
CofactorZinc.


CofactorsSubstratesProducts
KEGG-idC00038C99999C00354C00111C00118
CompoundZincMonovalent metalD-Fructose 1,6-bisphosphateGlycerone phosphateD-Glyceraldehyde 3-phosphate
Typeheavy metalunivalent metal (Na+, K+)carbohydrate,phosphate group/phosphate ioncarbohydrate,phosphate group/phosphate ioncarbohydrate,phosphate group/phosphate ion
1b57ABound:_ZN 360Bound:_NAUnboundAnalogue:PGHUnbound
1b57BBound:_ZN 360Bound:_NAUnboundAnalogue:PGHUnbound
1dosABound:_ZNUnboundUnboundUnboundUnbound
1dosBBound:_ZNUnboundUnboundUnboundUnbound
1zenABound:2x_ZNUnboundUnboundUnboundUnbound
1gynAAnalogue:_CD 401UnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P0AB71 & literature [8], [10] & [12]
pdbCatalytic residuesCofactor-binding residuescomment
1b57AASP 109;GLU 182;ASN 286
HIS 110;GLU 174;HIS 226;HIS 264(Catalytic zinc);VAL 225;GLY 227;GLY 265;SER 267(Monovalent metal)

1b57BASP 109;GLU 182;ASN 286
HIS 110;GLU 174;HIS 226;HIS 264(Catalytic zinc);VAL 225;GLY 227;GLY 265;SER 267(Monovalent metal)

1dosAASP 109;GLU 182;ASN 286
HIS 110;GLU 174;HIS 226;HIS 264(Catalytic zinc);VAL 225;GLY 227;GLY 265;SER 267(Monovalent metal)

1dosBASP 109;GLU 182;ASN 286
HIS 110;GLU 174;HIS 226;HIS 264(Catalytic zinc);VAL 225;GLY 227;GLY 265;SER 267(Monovalent metal)

1zenAASP 109;       ;ASN 286
HIS 110;GLU 174;HIS 226;HIS 264(Catalytic zinc);VAL 225;GLY 227;GLY 265;SER 267(Monovalent metal)
invisible 177-193
1gynAASP 109;       ;ASN 286
HIS 110;GLU 174;       ;HIS 264(Catalytic zinc);VAL 225;       ;GLY 265;SER 267(Monovalent metal)
invisible 177-193, 226-243

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.9, p.1203-12042
[5]p.250-251
[8]p.858-859
[9]Fig.5, p.157
[10]p.1307-1310
[12]Fig.6, p.389-3915
[13]Fig.3, p.852
[14]Fig.15
[18]Fig.2, p.137-1386

references
[1]
PubMed ID4324205
JournalBiochemistry
Year1971
Volume10
Pages1191-204
AuthorsMildvan AS, Kobes RD, Rutter WJ
TitleMagnetic resonance studies of the role of the divalent cation in the mechanism of yeast aldolase.
[2]
PubMed ID4607364
JournalBiochemistry
Year1974
Volume13
Pages4371-5
AuthorsHeron EJ, Caprioli RM
Title18O studies of the mechanisms of yeast and muscle aldolases.
[3]
PubMed ID1613797
JournalJ Mol Biol
Year1992
Volume225
Pages1137-41
AuthorsNaismith JH, Ferrara JD, Bailey S, Marshall K, Dauter Z, Wilson KS, Habash J, Harrop SJ, Berry AJ, Hunter WN
TitleInitiating a crystallographic study of a class II fructose-1,6-bisphosphate aldolase.
[4]
CommentsZINC-LIGANDS, AND MUTAGENESIS.
Medline ID93170474
PubMed ID8436219
JournalFEBS Lett
Year1993
Volume318
Pages11-6
AuthorsBerry A, Marshall KE
TitleIdentification of zinc-binding ligands in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli.
Related Swiss-protP0AB71
[5]
PubMed ID7872790
JournalArch Biochem Biophys
Year1995
Volume317
Pages244-52
AuthorsSzwergold BS, Ugurbil K, Brown TR
TitleProperties of fructose-1,6-bisphosphate aldolase from Escherichia coli: an NMR analysis.
[6]
PubMed ID8898912
JournalEur J Biochem
Year1996
Volume241
Pages243-8
AuthorsDe Montigny C, Sygusch J
TitleFunctional characterization of an extreme thermophilic class II fructose-1,6-bisphosphate aldolase.
[7]
PubMed ID9174952
JournalJ Mol Recognit
Year1996
Volume9
Pages652-7
AuthorsNicholls IA, Matsui J, Krook M, Mosbach K
TitleSome recent developments in the preparation of novel recognition systems: a recognition site for the selective catalysis of an aldol condensation using molecular imprinting and specific affinity motifs for alpha-chymotrypsin using a phage display peptide library.
[8]
CommentsX-RAY CRYSTALLOGRAPHY (1.67 ANGSTROMS).
Medline ID96433074
PubMed ID8836102
JournalNat Struct Biol
Year1996
Volume3
Pages856-62
AuthorsBlom NS, Tetreault S, Coulombe R, Sygusch J
TitleNovel active site in Escherichia coli fructose 1,6-bisphosphate aldolase.
Related PDB1dos
Related Swiss-protP0AB71
[9]
PubMed ID8771208
JournalProtein Sci
Year1996
Volume5
Pages154-61
AuthorsQamar S, Marsh K, Berry A
TitleIdentification of arginine 331 as an important active site residue in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli.
[10]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID97094986
PubMed ID8939754
JournalStructure
Year1996
Volume4
Pages1303-15
AuthorsCooper SJ, Leonard GA, McSweeney SM, Thompson AW, Naismith JH, Qamar S, Plater A, Berry A, Hunter WN
TitleThe crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding active site embedded in a familiar fold.
Related PDB1zen
Related Swiss-protP0AB71
[11]
PubMed ID9548961
JournalBiochemistry
Year1998
Volume37
Pages5746-54
AuthorsJohnson AE, Tanner ME
TitleEpimerization via carbon-carbon bond cleavage. L-ribulose-5-phosphate 4-epimerase as a masked class II aldolase.
[12]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID99182425
PubMed ID10080900
JournalJ Mol Biol
Year1999
Volume287
Pages383-94
AuthorsHall DR, Leonard GA, Reed CD, Watt CI, Berry A, Hunter WN
TitleThe crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity.
Related PDB1b57
Related Swiss-protP0AB71
[13]
PubMed ID9878448
JournalJ Mol Biol
Year1999
Volume285
Pages843-55
AuthorsPlater AR, Zgiby SM, Thomson GJ, Qamar S, Wharton CW, Berry A
TitleConserved residues in the mechanism of the E. coli Class II FBP-aldolase.
[14]
PubMed ID10712619
JournalEur J Biochem
Year2000
Volume267
Pages1858-68
AuthorsZgiby SM, Thomson GJ, Qamar S, Berry A
TitleExploring substrate binding and discrimination in fructose1, 6-bisphosphate and tagatose 1,6-bisphosphate aldolases.
[15]
PubMed ID11173490
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages310-3
AuthorsSauve V, Sygusch J
TitleCrystallization and preliminary X-ray analysis of native and selenomethionine fructose-1,6-bisphosphate aldolase from Thermus aquaticus.
[16]
PubMed ID11371431
JournalBiophys J
Year2001
Volume80
Pages2527-35
AuthorsOuporov IV, Knull HR, Huber A, Thomasson KA
TitleBrownian dynamics simulations of aldolase binding glyceraldehyde 3-phosphate dehydrogenase and the possibility of substrate channeling.
[17]
PubMed ID11237691
JournalProtein Expr Purif
Year2001
Volume21
Pages293-302
AuthorsSauve V, Sygusch J
TitleMolecular cloning, expression, purification, and characterization of fructose-1,6-bisphosphate aldolase from Thermus aquaticus.
[18]
PubMed ID11779234
JournalJ Mol Biol
Year2002
Volume315
Pages131-40
AuthorsZgiby S, Plater AR, Bates MA, Thomson GJ, Berry A
TitleA functional role for a flexible loop containing Glu182 in the class II fructose-1,6-bisphosphate aldolase from Escherichia coli.
[19]
PubMed ID12595741
JournalActa Crystallogr D Biol Crystallogr
Year2003
Volume59
Pages611-4
AuthorsHall DR, Kemp LE, Leonard GA, Marshall K, Berry A, Hunter WN
TitleThe organization of divalent cations in the active site of cadmium Escherichia coli fructose-1,6-bisphosphate aldolase.

comments
Although Glu174 is bound to the catalytic zinc ion, it moves away from the zinc ion to allow the substrate/product (Glycerone phosphate; GP) moiety to coordinate the ion during the catalysis (see [10]). Here, zinc ion functions as a Lewis acid electron sink, and polarizes the carbonyl bond of GP, for the elimination or addition reaction.
A monovalent cation is required for substrate binding, although it is not involved in catalysis.
According to the literature [18], although Glu182 is distant from the active site in the absence of substrate, it would be brought into a position to act as a general base on binding of substrates.
This enzyme catalyzes two reverse reactions, which are composed of two reactions respectively (see [12]):
(#1) the aldol condensation of a ketose, Glycerone phosphate (GP) and an aldose, glyceraldehyde 3-phosphate (G3P) to form the acyclic form of fructose 1,6-bisphospahte (FBP); that is addition of GP to the double-bond (carbonyl group) of G3P. (In Gluconeogenesis pathway)
(A) Isomerization:
(B) Addition of GP to the double-bond (carbonyl group) of G3P:
(#2) the clevage of FBP into GP and G3P; that is elimination of GP from FBP to form a new double-bond in another product, G3P. (In glycolysis pathway)
(C) Elimination of GP:
(D) Isomerization:
These catalytic reactions proceeds as follows (see [12] & [18]):
(A) Isomerization:
(A1) Carbonyl group and hydroxyl group of GP are bound to the catalytic zinc ion, replacing Glu174. Here, the zinc ion polarizes the carbonyl bond of the ketose substrate, GP, which increases the acidity of the hydroxymethylene (C1) hydrogen atoms, facilitating the next reaction, deprotonation.
(A2) Glu182 acts as a general base to deprotonate the C1 atom, leading to the formation of ene-diolate (carbanion) intermediate. This intermediate is stabilized by Asn286.
(B) Addition of the ene-diolate intermediate to the double-bond (carbonyl group) of G3P
(B1) The second substrate (aldehyde), G3P, which is electrophilic, binds to the active site, to interact with the nucleophilic ene-diolate intermediate. (The two planes of the ene-diolate nucleophile and the carbonyl acceptor must be nearly parallel for the C-C bond formation.) Here, Asp109 polarizes the addition site, the C1 carbonyl group of G3P (as a modulator).
(B2) The C1 atom of the ene-diolate intermediate makes a nucleophilic attack on the C1 carbonyl carbon of G3P, forming C-C bond. Here, Asp109 protonate the carbonyl oxygen of G3P, leading to formation of the hydroxyl group. At the same time, a carbonyl group is formed at the C2 carbon of the product, FBP.
On the other hand, the reverse reaction (C) proceeds as follows:
(C) Elimination of GP from FBP to form a new double-bond in G3P
(C1) The carbonyl oxygen (O2) and C3 hydroxyl group of FBP are bound to the catalytic zinc ion. This zinc ion polarizes the carbonyl bond of FBP.
(C2) Asp109 acts as a general base to deprotonate the C4 hydroxyl group of FBP (deprotonation site of leaving group), leading to the C-C bond cleavage. This cleavage gives the ene-diolate intermediate, which is bound to the catalytic zinc ion, and a leaving product, G3P. The ene-diolate intermediate is stabilized by Asn286.
(C3) G3P is released from the active site.
(D) Isomerization:
(D1) Glu182 acts as a general acid to protonate the C1 sp2 carbon of the intermediate, to form the carbonyl group at the C2 carbon.

createdupdated
2004-05-262009-02-26


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)

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