Summary: Fructose-bisphosphate aldolase class-II

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Fructose-bisphosphate aldolase Edit Wikipedia article

Fructose-bisphosphate aldolase

Identifiers

Databases

PDB structures

AmiGO / EGO

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PubMed	articles
NCBI	proteins

Fructose-bisphosphate aldolase class-I

fructose 1,6-bisphosphate aldolase from rabbit liver

Identifiers

Symbol

Glycolytic

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Fructose-bisphosphate aldolase class-II

class II fructose-1,6-bisphosphate aldolase in complex with phosphoglycolohydroxamate

Identifiers

Symbol

F_bP_aldolase

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

"Aldolase" redirects here. For other uses, see Aldolase (disambiguation).

Fructose-bisphosphate aldolase (EC 4.1.2.13), often just aldolase, is an enzyme catalyzing a reversible reaction that splits the aldol, fructose 1,6-bisphosphate, into the triose phosphates dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GAP). Aldolase can also produce DHAP from other (3S,4R)-ketose 1-phosphates such as fructose 1-phosphate and sedoheptulose 1,7-bisphosphate. Gluconeogenesis and the Calvin cycle, which are anabolic pathways, use the reverse reaction. Glycolysis, a catabolic pathway, uses the forward reaction. Aldolase is divided into two classes by mechanism.

[edit] Mechanism and structure

Class I proteins form a protonated Schiff base intermediate linking a highly conserved active site lysine with the DHAP carbonyl carbon. Class II proteins use a different mechanism which polarizes the carbonyl group with a divalent cation like Zn²⁺. The Escherichia coli galactitol operon protein, gatY, and N-acetyl galactosamine operon protein, agaY, which are tagatose-bisphosphate aldolase, are homologs of class II fructose-bisphosphate aldolase. Two histidine residues in the first half of the sequence of these homologs have been shown to be involved in binding zinc.^[1]

The protein subunits of both classes each have an Î±/Î² domain folded into a TIM barrel containing the active site. Several subunits are assembled into the complete protein. The two classes share little sequence identity.

With few exceptions only class I proteins have been found in animals, plants, and green algae.^[2] With few exceptions only class II proteins have been found in fungi. Both classes have been found widely in other eukaryotes and in bacteria. The two classes are often present together in the same organism. Plants and algae have plastidal aldolase, sometimes a relic of endosymbiosis, in addition to the usual cytosolic aldolase. A bifunctional fructose-bisphosphate aldolase/phosphatase, with class I mechanism, has been found widely in archaea and in some bacteria.^[3] The active site of this archaeal aldolase is also in a TIM barrel.

[edit] In gluconeogenesis and glycolysis

Gluconeogenesis and glycolysis share a series of six reversible reactions. In gluconeogenesis phosphoenolpyruvate (PEP) is reduced to fructose 1,6-bisphosphate with aldolase catalyzing the last reaction. In glycolysis fructose 1,6-bisphosphate is oxidized to PEP with aldolase catalyzing the first reaction. The aldolase used in gluconeogenesis and glycolysis is a cytoplasmic protein.

Three forms of class I protein are found in vertebrates. Aldolase A is preferentially expressed in muscle and brain; aldolase B in liver, kidney, and in enterocytes; and aldolase C in brain. Aldolases A and C are mainly involved in glycolysis, while aldolase B is involved in both glycolysis and gluconeogenesis.^[4] Some defects in aldolase B cause hereditary fructose intolerance. The metabolism of free fructose in liver exploits the ability of aldolase B to use fructose 1-phosphate as a substrate.^[5] Archaeal fructose-bisphosphate aldolase/phosphatase is presumably involved in gluconeogenesis because its product is fructose 6-phosphate.^[6]

[edit] In the Calvin cycle

The Calvin cycle is a carbon fixation pathway. It and gluconeogenesis share a series of four reversible reactions. In both pathways 3-phosphoglycerate (3-PGA or 3-PG) is reduced to fructose 1,6-bisphosphate with aldolase catalyzing the last reaction. A fifth reaction, catalyzed in both pathways by fructose 1,6-bisphosphatase, hydrolyzes the fructose 1-6-bisphosphate to fructose 6-phosphate and inorganic phosphate. The large decrease in free energy makes this reaction irreversible. In the Calvin cycle aldolase also catalyzes the production of sedoheptulose 1,7-bisphosphate from DHAP and erythrose 4-phosphate. The chief products of the Calvin cycle are triose phosphate (TP), which is a mixture of DHAP and GAP, and fructose 6-phosphate. Both are also needed to regenerate RuBP. The aldolase used by plants and algae in the Calvin cycle is usually a plastid-targeted protein encoded by a nuclear gene.

[edit] Reactions

Aldolase catalyzes

fructose 1,6-bisphosphate

DHAP + GAP

and also

sedoheptulose 1,7-bisphosphate

DHAP + erythrose 4-phosphate

fructose 1-phosphate

DHAP + glyceraldehyde

Aldolase is used in the reversible trunk of gluconeogenesis/glycolysis

2(PEP + NADH + H⁺ + ATP + H₂O)

fructose 1,6-bisphosphate + 2(NAD⁺ + ADP + P_i)

Aldolase is also used in the part of the Calvin cycle shared with gluconeogenesis, with the irreversible phosphate hydrolysis at the end catalyzed by fructose 1,6-bisphosphatase

2(3-PG + NADPH + H⁺ + ATP + H₂O)

fructose 1,6-bisphosphate + 2(NADP⁺ + ADP + P_i)

fructose 1,6-bisphosphate + H₂O â fructose 6-phosphate + P_i

In gluconeogenesis 3-PG is produced by enolase and phosphoglycerate mutase acting in series

PEP + H₂O

2-PG

3-PG

In the Calvin cycle 3-PG is produced by rubisco

RuBP + CO₂ + H₂O â 2(3-PG)

GAP is produced by phosphoglycerate kinase acting in series with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in gluconeogenesis, and in series with glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) in the Calvin cycle

3-PG + ATP

1,3-bisphosphoglycerate + ADP

1,3-bisphosphoglycerate + NAD(P)H + H⁺

GAP + P_i + NAD(P)⁺

Triose-phosphate isomerase maintains DHAP and GAP in near equilibrium, producing the mixture called triose phosphate (TP)

GAP

DHAP

Thus both DHAP and GAP are available to aldolase.

[edit] References

^ Zgiby SM, Thomson GJ, Qamar S, Berry A (2000). "Exploring substrate binding and discrimination in fructose1, 6-bisphosphate and tagatose 1,6-bisphosphate aldolases". Eur. J. Biochem. 267 (6): 1858â68. doi:10.1046/j.1432-1327.2000.01191.x. PMID 10712619.
^ Patron NJ, Rogers MB, Keeling PJ (2004). "Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates". Eukaryotic Cell 3 (5): 1169â75. doi:10.1128/EC.3.5.1169-1175.2004. PMC 522617. PMID 15470245. //www.ncbi.nlm.nih.gov/pmc/articles/PMC522617/.
^ Siebers B, Brinkmann H, DÃ¶rr C, Tjaden B, Lilie H, van der Oost J, Verhees CH (2001). "Archaeal fructose-1,6-bisphosphate aldolases constitute a new family of archaeal type class I aldolase". J. Biol. Chem. 276 (31): 28710â8. doi:10.1074/jbc.M103447200. PMID 11387336.
^ Walther EU, Dichgans M, Maricich SM, Romito RR, Yang F, Dziennis S, Zackson S, Hawkes R, Herrup K (1998). "Genomic sequences of aldolase C (Zebrin II) direct lacZ expression exclusively in non-neuronal cells of transgenic mice". Proc. Natl. Acad. Sci. U.S.A. 95 (5): 2615â20. PMC 19434. PMID 9482935. //www.ncbi.nlm.nih.gov/pmc/articles/PMC19434/.
^ Gopher A, Vaisman N, Mandel H, Lapidot A (1990). "Determination of fructose metabolic pathways in normal and fructose-intolerant children: a C-13 NMR study using C-13 fructose". Proc. Natl. Acad. Sci. U.S.A. 87 (14): 5449â53. PMC 54342. PMID 2371280. //www.ncbi.nlm.nih.gov/pmc/articles/PMC54342/.
^ Estelmann S, HÃ¼gler M, Eisenreich W, Werner K, Berg IA, Ramos-Vera WH, Say RF, Kockelkorn D, Gad'on N, Fuchs G (2011). "Labeling and enzyme studies of the central carbon metabolism in Metallosphaera sedula". J. Bacteriol. 193 (5): 1191â200. doi:10.1128/JB.01155-10. PMC 3067578. PMID 21169486. //www.ncbi.nlm.nih.gov/pmc/articles/PMC3067578/.

[edit] Further reading

Berry A, Marshall KE (February 1993). "Identification of zinc-binding ligands in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli". FEBS Lett. 318 (1): 11â6. doi:10.1016/0014-5793(93)81317-S. PMID 8436219.
Freemont PS, Dunbar B, Fothergill-Gilmore LA (February 1988). "The complete amino acid sequence of human skeletal-muscle fructose-bisphosphate aldolase". Biochem. J. 249 (3): 779â88. PMC 1148774. PMID 3355497. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1148774/.
Galkin A, Li Z, Li L, Kulakova L, Pal LR, Dunaway-Mariano D, Herzberg O (2009). "Structural insights into the substrate binding and stereoselectivity of giardia fructose-1,6-bisphosphate aldolase". Biochemistry 48 (14): 3186â96. doi:10.1021/bi9001166. PMC 2666783. PMID 19236002. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2666783/.
Marsh JJ, Lebherz HG (March 1992). "Fructose-bisphosphate aldolases: an evolutionary history". Trends Biochem. Sci. 17 (3): 110â3. doi:10.1016/0968-0004(92)90247-7. PMID 1412694.
Perham RN (April 1990). "The fructose-1,6-bisphosphate aldolases: same reaction, different enzymes". Biochem. Soc. Trans. 18 (2): 185â7. PMID 2199259.

[edit] External links

Tolan Laboratory at Boston University

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Fructose-bisphosphate aldolase class-II Provide feedback

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Literature references

Blom NS, Tetreault S, Coulombe R, Sygusch J; , Nat Struct Biol 1996;3:856-862.: Novel active site in Escherichia coli fructose 1,6-bisphosphate aldolase. PUBMED:8836102 EPMC:8836102

External database links

PANDIT:	PF01116
PROSITE:	PDOC00523
Pseudofam:	PF01116
SCOP:	1dos
SYSTERS:	F_bP_aldolase

This tab holds annotation information from the InterPro database.

InterPro entry IPR000771

Fructose-bisphosphate aldolase [PUBMED:2199259, PUBMED:1412694] is a glycolytic enzyme that catalyses the reversible aldol cleavage or condensation of fructose-1,6-bisphosphate into dihydroxyacetone-phosphate and glyceraldehyde 3-phosphate. There are two classes of fructose-bisphosphate aldolases with different catalytic mechanisms. Class-II aldolases [PUBMED:1412694], mainly found in prokaryotes and fungi, are homodimeric enzymes, which require a divalent metal ion, generally zinc, for their activity. This family also includes the Escherichia coli galactitol operon protein, gatY, which catalyses the transformation of tagatose 1,6-bisphosphate into glycerone phosphate and D-glyceraldehyde 3-phosphate; and E. coli N-acetyl galactosamine operon protein, agaY, which catalyses the same reaction. There are two histidine residues in the first half of the sequence of these enzymes that have been shown to be involved in binding a zinc ion [PUBMED:8436219].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function	aldehyde-lyase activity (GO:0016832)
Molecular function	zinc ion binding (GO:0008270)
Biological process	carbohydrate metabolic process (GO:0005975)

Domain organisation

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Pfam Clan

This family is a member of clan TIM_barrel (CL0036), which contains the following 57 members:

Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF1341 DUF2090 DUF556 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH iPGM_N MtrH NanE NAPRTase NeuB NMO OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PhosphMutase PRAI Pterin_bind QRPTase_C Racemase_4 RhaA Ribul_P_3_epim SOR_SNZ Tagatose_6_P_K ThiG TIM TIM-br_sig_trns TMP-TENI Transaldolase Trp_syntA UvdE UxuA

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	Seed (188)	Full (7516)	Representative proteomes				NCBI (4343)	Meta (1369)
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Curation

Seed source:

Prosite

Previous IDs:

none

Type:

Domain

Author:

Finn RD, Bateman A

Number in seed:

188

Number in full:

7516

Average length of the domain:

297.90 aa

Average identity of full alignment:

34 %

Average coverage of the sequence by the domain:

95.98 %

HMM information

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search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	25.4	25.4
Trusted cut-off	25.7	25.7
Noise cut-off	25.0	25.2

Model length:

287

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15

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F_bP_aldolase

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the F_bP_aldolase domain has been found. There are 71 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: F_bP_aldolase (PF01116)

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Summary: Fructose-bisphosphate aldolase class-II

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Fructose-bisphosphate aldolase Edit Wikipedia article

Contents

[edit] Mechanism and structure

[edit] In gluconeogenesis and glycolysis

[edit] In the Calvin cycle

[edit] Reactions

[edit] References

[edit] Further reading

[edit] External links

Fructose-bisphosphate aldolase class-II Provide feedback

Literature references

External database links

InterPro entry IPR000771

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Alignment types

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Trees

Curation and family details

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Species distribution

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How the sunburst is generated

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Sub-species

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Annotation

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Selected sequences

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Interactions

Structures