Aldolase

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Revision as of 10:53, 9 June 2011

Ligands:

Activity:

Fructose-bisphosphate aldolase, with EC number 4.1.2.13

Structural annotation:
Resources:	CATH : 4Alda00 InterPro : Ipr013785, Ipr000741 Pfam : PF00274 SCOP : d4alda_

Evolutionary conservation:

Toggle Conservation Colors:	Rows = identical sequences:
Further Information:	Caveats, Explanation, Complete Results at ConSurfDB

Resources:

FirstGlance, OCA, RCSB, PDBsum

Coordinates:

save as pdb, mmCIF, xml

1 Fructose Bisphosphate Aldolase

Fructose Bisphosphate Aldolase

Introduction and Structure

Fructose bisphosphate aldolase is an enzyme in glycolysis and gluconeogenesis. Glycolyis is responsible for the conversion of glucose into two three-carbon pyruvate molecules without the need for oxygen. The process generates two net ATP. The overall reaction is:

Glucose + 2 NAD+ + 2 ADP + 2 Pi --> 2 pyruvate (3-carbon product) + 2 NADH + 2 ATP + 2 H20 + 4 H+

Gluconeogenesis is responsible for maintaining the appropriate levels of blood glucose in animals by generating glucose from non-carbohydrate precursors. Gluconeogenesis can make glucose from lactate, pyruvate, citric acid cycle intermediates and from most amino acids (the exceptions being leucine and lysine). The common intermediate for all of the precursors on their way to becoming glucose must be oxaloacetate.

The aldolase catalyzes the reversible cleavage of fructose-1,6-bisphosphate into dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GAP). Different isozymes of aldolase can also catalyze the cleavage of fructose 1-phosphate to diydroxyacetone and glyceraldehyde (GA). Different isozymes exhibit preferences for either or both of the substrates, depending on the role of the aldolase (i.e. gluconeogenesis versus glycolysis).^[1]

While it can exist as a monomer, it normally exists as a . The enzyme is an a/B protein with a TIM beta/alpha beta fold. The fold designation is based upon the nine alpha helices and eight parallel beta sheets in a closed barrel of each monomeric subunit. It is part of the aldolase superfamily and the class I aldolases.^[2] can be seen in their specific regions mostly concentric to the active site, represented by the blue and red residues.

Although some form of fructose bisphosphate aldolase is present in nearly all living things, certain isoforms carry a large degree of conservation. The enzyme from rabbit muscle has nearly the tertiary and primary structure as the enzyme in human muscle. As a result, implications from rabbit muscle aldolase also reveal a great deal about the human forms of the enzyme. ^[3]

Binding and Catalysis

As an enzyme, the aldolase must not only encourage and favor the hydrolysis of fructose 1,6-bisphosphate, but also bind the substrate so as to hold it in the active site. The main-chain nitrogens of Ser271 and Gly272 hold the 1-phosphate group while the Lys41, Arg42 and Arg303 residues hold the 6-phosphate group. The five proposed binding residues are in close proximity to the catalytic Lys229, implicating them as participants in the binding process.^[4] The , which sits just outside of the barrel and catalytic site, of the enzyme also appears to contribute to the catalytic process of the aldolase. Mutations or suppression of the final tyrosine residue (Tyr363) causes a notable drop in the activity of the enzyme. Two cysteine residues have also been implicated in the catalytic process. Though they do not appear to be necessary for catalysis, modification of them does result in a decrease in catalytic activity. The two Cys residues are far from the active site, but do impact the movement of the C-terminus of the enzyme, which further implicates the terminus as participatory in the catalysis.

The reaction is an aldol cleavage, or otherwise termed, retro aldo condensation. Catalysis occurs first when the nucleophilic ε-amine group of Lys229 attacks the carbonyl carbon of the substrate (FBP) in its open-ring state, pushing an electron pair to the oxygen of the carbonyl. The oxygen is protonated and leaves as water as a protonated is produced (an imine resulting from a ketone and amine) with the open-ring form of FBP, accompanied by electrostatic stabilization from Aldol cleavage between C3 and C4 produces GAP and an enamine precursor to DHAP.^[1] The cleavage is facilitated by the positive charge from the Schiff base. The subsequent electron movement, which alleviates the positive charge, also breaks the C3-C4 bond.^[3] Tautomerization, protonation and the hydrolysis of the Schiff base produce the final product of DHAP and regenerate the enzyme. The catalysis is driven by the more favorable stability of the protonated Schiff base compared to the enolate that would appear in basic catalysis pathways.^[1]

Kinetics

Isotopic labelling has revealed the rate-determining step for the reaction. Either the carbon-carbon bond cleavage or the release of glyceraldehyde-3-phosphate comprise the slow step of the catalysis reaction; however, studies do indicate that the GAP release is likely the slowest step.^[3]

It has been shown that aldolase is inhibited allosterically by oxidized glutathione, which is an oxidizing species biologically present. The glutathione oxidizes a thiol 25 angstroms from the catalytic site, which subsequently causes a drop in catalytic activity. In addition, the enzyme shows no positive cooperativity, despite being an oligomer. In fact, kinetics data actually show that the enzyme exhibits negative cooperativity. Thus the catalysis is highly compartmentalized within each subunit and binding causes little distal change of the enzymes structure.^[5]

Regulation

The regulation of fructose 1,6-bisphosphate aldolase is not well understood, but the understanding is every-increasing. As it is currently observed, aldolase C appears to be regulated mainly by the gene expression--the concentration of mRNA in the cytoplasm.^[6] It is also known that adenosine 3',5'-cyclicmonophosphate (cAMP) affects the expression of the gene. cAMP concentration has been positively correlated with aldolase C expression. It is believed that cAMP acts upon a section of the promotor region, distal element D, causing the transcriptional promoter, NGFI-B, to bind. Once bound, the promoter activates the transcription of the gene coding for fructose bisphosphate aldolase.^[7] Given the inhibitory effects of an oxidant in the presence of aldolase, it is possible that this could be a mechanism of regulation of the enzyme. The deactivation that accompanies the oxidation of the surface thiol of Cys72 could be used intracellularly to slow the catalysis of the enzyme and regulate glycolysis.^[5]

3D structures of Aldolase

Update June 2011

Fructose–1,6-bisphosphate aldolase

1ojx, 1ok6 – TptFBPA – Thermoproteus tenax
3qrh – EncFBPA – Encephalitozoon cuniculi
3qm3 - FBPA – Campylobacter jejuni
3q94 – FBPA – Bacullus anthracis
3c4u– HpFBPA – Helicobacter pylori
1zah, 1fdj, 1ewd, 1ewe, 1ex5, 1ado - rFBPA – rabbit
3dfn, 3dfp, 3dfq, 3dft, 2bv4, 3b8d, 3bv4 – rFBPA (mutant)
3kx6 – FBPA – Babesia bovis
3gak – GiFBPA – Giardia intestinalis
3ekl, 3ekz – MtFBPA – Mycobacterium tuberculosis
2qap, 1epx – LmFBPA – Leishmania mexicana
1a5c – PfFBPA – Plasmodium falciparum
2iqt – FBPA – Porphyromonas gingivalis
2fjk – FBPA – Thermus caldophilus
1xfb, 1qo5, 2ald, 1ald – hFBPA – human
1xdl, 1xdm – hFBPA (mutant)
1gyn, 1l6w, 1dos, 1zen – EcFBPA - Escherichia coli
1f2j – FBPA – Trypanosoma brucei
1fba – FBPA – Drosophila melanogaster

FBPA binary complex

2yce, 1ok4 – TptFBPA + reaction intermediate

1w8s – TptFBPA + FBP

3mbd – EncFBPA + phosphate

3mbf - EncFBPA + FBP

3n9r, 3n9s, 3c52, 3c56 - HpFBPA + inhibitor

3mmt – FBPA + FBP – Bartonella henselae

1zai - rFBPA + FBP

6ald - rFBPA (mutant) + FBP

2quv - rFBPA + phosphate

2qut - rFBPA + reaction intermediate

3dfo, 3dfs, 2quu - rFBPA (mutant) + reaction intermediate

1j4e - rFBPA (mutant) + substrate

2ot0 – rFBPA + Wiskott-Aldrich syndrome protein C-terminal

2ot1, 1zaj, 1zal – rFBPA + inhibitor

3lge – rFBPA + Sorting Nexin-9

3gay – GiFBPA + inhibitor

3gb6 – GiFBPA + FBP

2isv, 2isw - GiFBPA + oxamate

3elf – MtFBPA + FBP

2qdg - LmFBPA + FBP

2qdh – LmFBPA + inhibitor

2eph, 2pc4 – PfFBPA + BPTRAP C-terminal

4ald – hFBPA + FBP

1rv8, 1rvg – FBPA + metal – Thermus aquaticus

1b57 – EcFBPA + oxamate

Tagatose–1,6-bisphosphate aldolase

3myo, 3myp, 3mhf, 3jrk – SpTBPA – Streptococcus pyogenes 3iv3 - TBPA – Streptococcus mutans 3mhg - SpTBPA + reaction intermediate

3kao – SaTBPA – Staphylococcus aureus

1gvf - EcTBPA

Fuculose–1-phosphate aldolase

2opi – FPA – Bacteroides thetaiotaomicron

2flf, 2fk5 – TtFPA - Thermus thermophilus

1fua, 2fua, 3fua – EcFPA

1e46, 1e47, 1e48, 1e49, 1e4a, 1e4b, 1e4c, 1dzu, 1dzw, 1dzx, 1dzy, 1dzz, 1dzv – EcFPA (mutant)

4fua – EcFPA + oxamate

Deoxyribose-phosphate aldolase

3r12, 3r13, 1pvt, 1o0y – TmDERA – Thermotoga maritima

3ndo – MsDERA – Mycobacterium smegmatis

3ng3 – MsDERA + aldehyde

2a4a – DERA – Plasmodium yoelii

1vcv – DERA – Pyrobaculum aerophilum

1p1x, 1ktn, 3npu, 3npv, 3npw, 3npx, 3nq2, 3nq8, 3nqv, 3nr0, 3q2d – EcDERA

1jcj, 1jcl – EcDERA (mutant) + reaction intermediate

1n7k – ApDERA – Aeropyrum pernix

1mzh – AaDERA - Aquifex aeolicus 3ngj – DERA – Entamoeba histolytica

Dehydroneopterin aldolase

3r2e – DHNPA – Yersinia pestis 2cg8 – DHNPA – Streptococcus pneumoniae 2o90 – EcDHNPA + neopterin

2nm2, 2nm3, 1u68, 2dhn - SaDHNPA + neopterin

1rri, 1rrw, 1rry, 1rs2, 1rs4, 1rsd, 1rsi, 1dhn - SaDHNPA + inhibitor

1z9w – MtDHNPA

1sql – DHNPA + guanine – Arabidopsis thaliana

HPCH/HPAI aldolase

3qz6 – HPA – Desulfitobacterium hafniense

2v5j – EcHPA

2v5k – EcHPA + oxamate

Sialic acid aldolase

3lbm – EcSAA

3lcf, 3lcg, 3lch, 3lci, 3lcl, 2wnq, 2wo5 - EcSAA (mutant)

3lbc – EcSAA + L-arabinose

2wnn – EcSAA + pyruvate
2wnz, 2wkj - EcSAA (mutant) + pyruvate
2wpb - EcSAA (mutant) + pyruvate + inhibitor

3lcx - EcSAA L-KDO (mutant)

3lcw - EcSAA L-KDO (mutant) + hydroxypyruvate

Oxoadipate aldolase

3noj – PpCHA-ALD – Pseudomonas putida

Oxovalerate aldolase

1nvm – OVA + acetaldehyde dehydrogenase - Pseudomonas

Deoxydephosphogluconate aldolase

3nzr – DDPGA – Vibrio fischeri

2r91, 2r94 – TptDDPGA

2yw3, 2yw4 – TtDDPGA

2nuw, 2nux – SaDDPGA – Sulfolobus acidocaldarius

1vlw – TmDDPGA

1w37 - SsDDPGA – Sulfolobus solfataricus

1mxs, 1kga – PpDDPGA

1eun, 1fq0 – EcDDPGA

1fwr - EcDDPGA (mutant)

   DDPGA complex

1nuy – SaDDPGA + pyruvate
1wa3 - TmDDPGA + pyruvate
1w3i - SsDDPGA + pyruvate
1w3n - SsDDPGA + gluconate

1w3t - SsDDPGA + gluconate + pyruvate
1eua - EcDDPGA + pyruvate

Deoxydephosphooctonate aldolase

3e0i, 2nxi, 1fx6 – AaDDPOA

2ef9, 2nws, 2nx1, 2nx3, 2nxg, 2nxh, 1t99 – AaDDPOA (mutant)

1x8f – EcDDPOA

3fs2 – DDPOA – Bruciella melitensis

3e9a – DDPOA – Vibrio cholerae

2qkf – NmDDPOA – Neisseria meningitides 3qpy, 3qpz, 3qq0, 3qq1 – NmDDPOA (mutant) 1o60 - DDPOA – Haemophilus influenzae

   DDPOA binary complex

1fxp – AaDDPOA + Cd

1pck, 1fwn, 1fws - AaDDPOA + PEP

1pcw, 1pe1, 1jcx - AaDDPOA + inhibitor

1lrn - AaDDPOA (mutant) + Cd

2nwr, 1t96, 1lro - AaDDPOA (mutant) + PEP

3e12 – AaDDPOA + KDO8P

1x6u - EcDDPOA + KDO8P

1q3n - EcDDPOA + PEP

1phq, 1phw, 1pl9 - EcDDPOA + substrate analog

   DDPOA tertiary complex

1fy6 - AaDDPOA + arabinose + Cd

1jcy, 1fwt, 1fww, 1fxq - AaDDPOA + PEP + sugar

2a2i, 1zha, 1zji, 1t8x, 1lrq - AaDDPOA (mutant) + PEP + arabinose

2a21 - AaDDPOA + PEP + phosphate

Deoxydephosphogalactonate aldolase

2v81 – EcKDPGAL

2c0a – EcKDPGAL (mutant)

2v82 – EcKDPGAL + 2-keto-deoxy-galactose

Deoxydephosphoheptonate aldolase

1vr6 – TmKDPHAL

Deoxygalactarate aldolase

1dxe – EcDGA

1dxf – EcDGA + pyruvate

Aldolase class II

3ocr – ALDII – Pseudomonas syringae

2vws – EcALDII

2vwt – EcALDII + pyruvate

Sphingosin-1-phosphate aldolase

3mc6 – SCDPL1 (mutant) – yeast

Rhamnulose-1-phosphate aldolase

1gt7 – EcRPA

2v9g, 2v9o, 2uyu, 2uyv, 2v9e, 2v9f, 2v9i, 2v9l, 2v9m, 2v9n, 2v29, 2v2a, 2v2b, 1ojr – EcRPA (mutant)

Oxoglutarate aldolase

3m6y – OGA – Bacillus cereus

1wau, 1wbh – EcOGA (mutant)

LsrF aldolase

3gkf – EcLsrFA

3glc, 3gnd – EcLsrFA + ribose derivative

Threonine aldolase

2fm1, 1m6s, 1jg8 – TmThrA

1lw4, 1lw5 – TmThrA + amino acid

1svv – ThrA – Leishmania major

Phenylserine aldolase

1v72 – PpFSA

1j2w, 1ub3 - TtALD

Additional Resources

For additional information, see: Carbohydrate Metabolism

References

↑ ^1.0 ^1.1 ^1.2 Voet, D, Voet, J, & Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley & Sons, Inc.
↑ Protein: fructose-1,6-bisphosphate aldolase from human (homo sapiens), muscle isozyme. (2009). Retrieved from http://scop.mrc-lmb.cam.ac.uk
↑ ^3.0 ^3.1 ^3.2 Gefflaut, T., B. Casimir, J. Perie, and M. Willson. "Class I Aldolases: Substrate Specificity, Mechanism, Inhibitors and Structural Aspects." Prog. Biophys. molec. Biol.. 63. (1995): 301-340.
↑ Dalby A, Dauter Z, Littlechild JA. Crystal structure of human muscle aldolase complexed with fructose 1,6-bisphosphate: mechanistic implications. Protein Sci. 1999 Feb;8(2):291-7. PMID:10048322
↑ ^5.0 ^5.1 Sygusch, J., and Beaudry, D. "Allosteric communication in mammalian muscle aldolase." Biochem. J.. 327. (1997): 717-720.
↑ Paolella, G, Buono, P, Mancini, F P, Izzo, P, and Salvatore, F. "Structure and expression of mouse aldolase genes." Eur. J. Biochem.. 156. (1986): 229-235.
↑ Buono, P, Cassano, S, Alfieri, A, Mancini, A, and Salvatore, F. "Human aldolase C gene expression is regulated by adenosine 30,50-cyclic monophosphate (cAMP) in PC12 cells." Gene. 291. (2002): 115-121.

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@@ Line 45: / Line 45: @@
 ===Fructose–1,6-bisphosphate aldolase===
-[[1ojx]], [[1ok6]] – TptFBPA – ''Thermoproteus tenax''
+[[1ojx]], [[1ok6]] – TptFBPA – ''Thermoproteus tenax''<br />
+[[3qrh]] – EncFBPA – ''Encephalitozoon cuniculi''<br />
+[[3qm3]] - FBPA – ''Campylobacter jejuni''<br />
+[[3q94]] – FBPA – ''Bacullus anthracis''<br />
+[[3c4u]]– HpFBPA – ''Helicobacter pylori''<br />
+[[1zah]], [[1fdj]], [[1ewd]], [[1ewe]], [[1ex5]], [[1ado]] - rFBPA – rabbit<br />
+[[3dfn]], [[3dfp]], [[3dfq]], [[3dft]], [[2bv4]], [[3b8d]], [[3bv4]] – rFBPA (mutant)<br />
+[[3kx6]] – FBPA – ''Babesia bovis''<br />
+[[3gak]] – GiFBPA – ''Giardia intestinalis''<br />
+[[3ekl]], [[3ekz]] – MtFBPA – ''Mycobacterium tuberculosis''<br />
+[[2qap]], [[1epx]] – LmFBPA – ''Leishmania mexicana''<br />
+[[1a5c]] – PfFBPA – ''Plasmodium falciparum''<br />
+[[2iqt]] – FBPA – ''Porphyromonas gingivalis''<br />
+[[2fjk]] – FBPA – ''Thermus caldophilus''<br />
+[[1xfb]], [[1qo5]], [[2ald]], [[1ald]] – hFBPA – human<br />
+[[1xdl]], [[1xdm]] – hFBPA (mutant)<br />
+[[1gyn]], [[1l6w]], [[1dos]], [[1zen]] – EcFBPA - ''Escherichia coli''<br />
+[[1f2j]] – FBPA – ''Trypanosoma brucei''<br />
+[[1fba]] – FBPA – ''Drosophila melanogaster''<br />
-[[3qrh]] – EncFBPA – ''Encephalitozoon cuniculi''
+===FBPA binary complex===
-[[3qm3]] - FBPA – ''Campylobacter jejuni''
-[[3q94]] – FBPA – ''Bacullus anthracis''
-[[3c4u]]– HpFBPA – ''Helicobacter pylori''
-[[1zah]], [[1fdj]], [[1ewd]], [[1ewe]], [[1ex5]], [[1ado]] - rFBPA – rabbit
-[[3dfn]], [[3dfp]], [[3dfq]], [[3dft]], [[2bv4]], [[3b8d]] – rFBPA (mutant)
-[[3kx6]] – FBPA – ''Babesia bovis''
-[[3gak]] – GiFBPA – ''Giardia intestinalis''
-[[3ekl]], [[3ekz]] – MtFBPA – ''Mycobacterium tuberculosis''
-[[2qap]], [[1epx]] – LmFBPA – ''Leishmania mexicana''
-[[1a5c]] – PfFBPA – ''Plasmodium falciparum''
-[[2iqt]] – FBPA – ''Porphyromonas gingivalis''
-[[2fjk]] – FBPA – ''Thermus caldophilus''
-[[1xfb]], [[1qo5]], [[2ald]], [[1ald]] – hFBPA – human
-[[1xdl]], [[1xdm]] – hFBPA (mutant)
-[[1gyn]], [[1l6w]], [[1dos]], [[1zen]] – EcFBPA - ''Escherichia coli''
-[[1f2j]] – FBPA – ''Trypanosoma brucei''
-[[1fba]] – FBPA – ''Drosophila melanogaster''
-    ''FBPA binary complex''
 [[2yce]], [[1ok4]] – TptFBPA + reaction intermediate
@@ Line 137: / Line 119: @@
 ===Tagatose–1,6-bisphosphate aldolase===
-[[3myo]], [[3myp]], [[3mhf]]– SpTBPA – ''Streptococcus pyogenes''
+[[3myo]], [[3myp]], [[3mhf]], [[3jrk]] – SpTBPA – ''Streptococcus pyogenes''
+[[3iv3]] - TBPA – ''Streptococcus mutans''
 [[3mhg]] - SpTBPA + reaction intermediate
@@ Line 153: / Line 135: @@
 [[1fua]], [[2fua]], [[3fua]] – EcFPA
-[[1e46]], [[1e47]], [[1e48]], [[1e49]], [[1e4a]], [[1e4b]], [[1e4c]], [[1dzu]], [[1dzw]], [[1dzx]], [[1dzy]], [[1dzz]] – EcFPA (mutant)
+[[1e46]], [[1e47]], [[1e48]], [[1e49]], [[1e4a]], [[1e4b]], [[1e4c]], [[1dzu]], [[1dzw]], [[1dzx]], [[1dzy]], [[1dzz]], [[1dzv]] – EcFPA (mutant)
 [[4fua]] – EcFPA + oxamate
@@ Line 159: / Line 141: @@
 ===Deoxyribose-phosphate aldolase===
-[[3r12]], [[3r13]], [[1pvt]], [[1o0y]] – TmDERA – ''Thermotoga maritime''
+[[3r12]], [[3r13]], [[1pvt]], [[1o0y]] – TmDERA – ''Thermotoga maritima''
 [[3ndo]] – MsDERA – ''Mycobacterium smegmatis''
@@ Line 169: / Line 151: @@
 [[1vcv]] – DERA – ''Pyrobaculum aerophilum''
-[[1p1x]] – EcDERA
+[[1p1x]], [[1ktn]], [[3npu]], [[3npv]], [[3npw]], [[3npx]], [[3nq2]], [[3nq8]], [[3nqv]], [[3nr0]], [[3q2d]]  – EcDERA
 [[1jcj]], [[1jcl]] – EcDERA (mutant) + reaction intermediate
-[[1n7k]] – DERA – ''Aeropyrum pernix''
+[[1n7k]] – ApDERA – ''Aeropyrum pernix''
 [[1mzh]] – AaDERA - ''Aquifex aeolicus''
+[[3ngj]] – DERA – ''Entamoeba histolytica''
 ===Dehydroneopterin aldolase===
 [[3r2e]] – DHNPA – ''Yersinia pestis''
+[[2cg8]] – DHNPA – ''Streptococcus pneumoniae''
 [[2o90]] – EcDHNPA + neopterin
@@ Line 265: / Line 248: @@
 [[3e9a]] – DDPOA – ''Vibrio cholerae''
-[[2qkf]] – DDPOA – ''Neisseria meningitides''
+[[2qkf]] – NmDDPOA – ''Neisseria meningitides''
+[[3qpy]], [[3qpz]], [[3qq0]], [[3qq1]] – NmDDPOA (mutant)
+[[1o60]] - DDPOA – ''Haemophilus influenzae''
     ''DDPOA binary complex''