DB code: S00235

RLCP classification 8.131.708000.451 : Isomerization
4.151.766500.451 : Addition
5.151.2325000.451 : Elimination
8.113.915300.451 : Isomerization
CATH domain 3.20.20.70 : TIM Barrel Catalytic domain
E.C. 4.1.2.13
CSA 1b57
M-CSA 1b57
MACiE M0052

CATH domain Related DB codes (homologues)
3.20.20.70 : TIM Barrel S00215 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0AB71 Fructose-bisphosphate aldolase class 2
FBP aldolase
FBPA
EC 4.1.2.13
Fructose-bisphosphate aldolase class II
Fructose-1,6-bisphosphate aldolase
NP_417400.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491125.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01116 (F_bP_aldolase)
[Graphical View]

KEGG enzyme name
fructose-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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0AB71 ALF_ECOLI D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate. Homodimer. Zinc.

KEGG Pathways
Map code Pathways E.C.
MAP00010 Glycolysis / Gluconeogenesis
MAP00030 Pentose phosphate pathway
MAP00051 Fructose and mannose metabolism
MAP00710 Carbon fixation in photosynthetic organisms

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C99999 C00354 C00111 C00118
E.C.
Compound Zinc Monovalent metal D-Fructose 1,6-bisphosphate Glycerone phosphate D-Glyceraldehyde 3-phosphate
Type heavy metal univalent metal (Na+, K+) carbohydrate,phosphate group/phosphate ion carbohydrate,phosphate group/phosphate ion carbohydrate,phosphate group/phosphate ion
ChEBI 29105
37736
16108
29052
PubChem 32051
172313
668
439168
1b57A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN_360 Bound:_NA Unbound Analogue:PGH Unbound
1b57B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN_360 Bound:_NA Unbound Analogue:PGH Unbound
1dosA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
1dosB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
1zenA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound
1gynA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_CD_401 Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P0AB71 & literature [8], [10] & [12]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1b57A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 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)
1b57B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 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)
1dosA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 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)
1dosB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 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)
1zenA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 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
1gynA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 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
References Sections No. of steps in catalysis
[1]
Fig.9, p.1203-1204 2
[5]
p.250-251
[8]
p.858-859
[9]
Fig.5, p.157
[10]
p.1307-1310
[12]
Fig.6, p.389-391 5
[13]
Fig.3, p.852
[14]
Fig.1 5
[18]
Fig.2, p.137-138 6

References
[1]
Resource
Comments
Medline ID
PubMed ID 4324205
Journal Biochemistry
Year 1971
Volume 10
Pages 1191-204
Authors Mildvan AS, Kobes RD, Rutter WJ
Title Magnetic resonance studies of the role of the divalent cation in the mechanism of yeast aldolase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 4607364
Journal Biochemistry
Year 1974
Volume 13
Pages 4371-5
Authors Heron EJ, Caprioli RM
Title 18O studies of the mechanisms of yeast and muscle aldolases.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1613797
Journal J Mol Biol
Year 1992
Volume 225
Pages 1137-41
Authors Naismith JH, Ferrara JD, Bailey S, Marshall K, Dauter Z, Wilson KS, Habash J, Harrop SJ, Berry AJ, Hunter WN
Title Initiating a crystallographic study of a class II fructose-1,6-bisphosphate aldolase.
Related PDB
Related UniProtKB
[4]
Resource
Comments ZINC-LIGANDS, AND MUTAGENESIS.
Medline ID 93170474
PubMed ID 8436219
Journal FEBS Lett
Year 1993
Volume 318
Pages 11-6
Authors Berry A, Marshall KE
Title Identification of zinc-binding ligands in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli.
Related PDB
Related UniProtKB P0AB71
[5]
Resource
Comments
Medline ID
PubMed ID 7872790
Journal Arch Biochem Biophys
Year 1995
Volume 317
Pages 244-52
Authors Szwergold BS, Ugurbil K, Brown TR
Title Properties of fructose-1,6-bisphosphate aldolase from Escherichia coli: an NMR analysis.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8898912
Journal Eur J Biochem
Year 1996
Volume 241
Pages 243-8
Authors De Montigny C, Sygusch J
Title Functional characterization of an extreme thermophilic class II fructose-1,6-bisphosphate aldolase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9174952
Journal J Mol Recognit
Year 1996
Volume 9
Pages 652-7
Authors Nicholls IA, Matsui J, Krook M, Mosbach K
Title Some 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.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.67 ANGSTROMS).
Medline ID 96433074
PubMed ID 8836102
Journal Nat Struct Biol
Year 1996
Volume 3
Pages 856-62
Authors Blom NS, Tetreault S, Coulombe R, Sygusch J
Title Novel active site in Escherichia coli fructose 1,6-bisphosphate aldolase.
Related PDB 1dos
Related UniProtKB P0AB71
[9]
Resource
Comments
Medline ID
PubMed ID 8771208
Journal Protein Sci
Year 1996
Volume 5
Pages 154-61
Authors Qamar S, Marsh K, Berry A
Title Identification of arginine 331 as an important active site residue in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID 97094986
PubMed ID 8939754
Journal Structure
Year 1996
Volume 4
Pages 1303-15
Authors Cooper SJ, Leonard GA, McSweeney SM, Thompson AW, Naismith JH, Qamar S, Plater A, Berry A, Hunter WN
Title The 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 PDB 1zen
Related UniProtKB P0AB71
[11]
Resource
Comments
Medline ID
PubMed ID 9548961
Journal Biochemistry
Year 1998
Volume 37
Pages 5746-54
Authors Johnson AE, Tanner ME
Title Epimerization via carbon-carbon bond cleavage. L-ribulose-5-phosphate 4-epimerase as a masked class II aldolase.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 99182425
PubMed ID 10080900
Journal J Mol Biol
Year 1999
Volume 287
Pages 383-94
Authors Hall DR, Leonard GA, Reed CD, Watt CI, Berry A, Hunter WN
Title The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity.
Related PDB 1b57
Related UniProtKB P0AB71
[13]
Resource
Comments
Medline ID
PubMed ID 9878448
Journal J Mol Biol
Year 1999
Volume 285
Pages 843-55
Authors Plater AR, Zgiby SM, Thomson GJ, Qamar S, Wharton CW, Berry A
Title Conserved residues in the mechanism of the E. coli Class II FBP-aldolase.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10712619
Journal Eur J Biochem
Year 2000
Volume 267
Pages 1858-68
Authors Zgiby SM, Thomson GJ, Qamar S, Berry A
Title Exploring substrate binding and discrimination in fructose1, 6-bisphosphate and tagatose 1,6-bisphosphate aldolases.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11173490
Journal Acta Crystallogr D Biol Crystallogr
Year 2001
Volume 57
Pages 310-3
Authors Sauve V, Sygusch J
Title Crystallization and preliminary X-ray analysis of native and selenomethionine fructose-1,6-bisphosphate aldolase from Thermus aquaticus.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11371431
Journal Biophys J
Year 2001
Volume 80
Pages 2527-35
Authors Ouporov IV, Knull HR, Huber A, Thomasson KA
Title Brownian dynamics simulations of aldolase binding glyceraldehyde 3-phosphate dehydrogenase and the possibility of substrate channeling.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11237691
Journal Protein Expr Purif
Year 2001
Volume 21
Pages 293-302
Authors Sauve V, Sygusch J
Title Molecular cloning, expression, purification, and characterization of fructose-1,6-bisphosphate aldolase from Thermus aquaticus.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11779234
Journal J Mol Biol
Year 2002
Volume 315
Pages 131-40
Authors Zgiby S, Plater AR, Bates MA, Thomson GJ, Berry A
Title A functional role for a flexible loop containing Glu182 in the class II fructose-1,6-bisphosphate aldolase from Escherichia coli.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 12595741
Journal Acta Crystallogr D Biol Crystallogr
Year 2003
Volume 59
Pages 611-4
Authors Hall DR, Kemp LE, Leonard GA, Marshall K, Berry A, Hunter WN
Title The organization of divalent cations in the active site of cadmium Escherichia coli fructose-1,6-bisphosphate aldolase.
Related PDB
Related UniProtKB

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.

Created Updated
2004-05-26 2009-02-26