biochem480 [Spring 2018] Enzyme Bio-informatics project

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1 biochem480 [Spring 2018] Enzyme Bio-informatics project Student Name: Alissa Burbridge Enzyme Name: Fructose-bisphosphate aldolase # of PDB entries for this enzyme: 129 PDB code: 4ALD E.C. # Authors of paper of PDB data: Dalby,A.R, Dauter, Z., Littlechild,J.A Journal Reference: (1999) Protein Sci. 8: Pub Med Abstract of paper: Fructose 1,6-bisphosphate aldolase catalyzes the reversible cleavage of fructose 1,6- bisphosphate and fructose 1-phosphate to dihydroxyacetone phosphate and either glyceraldehyde 3-phosphate or glyceraldehyde, respectively. Catalysis involves the formation of a Schiff's base intermediate formed at the epsilon-amino group of Lys229. The existing apoenzyme structure was refined using the crystallographic free-r-factor and maximum likelihood methods that have been shown to give improved structural results that are less subject to model bias. Crystals were also soaked with the natural substrate (fructose 1,6-bisphosphate), and the crystal structure of this complex has been determined to 2.8 A. The apo structure differs from the previous Brookhaven-deposited structure (1ald) in the flexible C-terminal region. This is also the region where the native and complex structures exhibit differences. The conformational changes between native and complex structure are not large, but the observed complex does not involve the full formation of the Schiff's base intermediate, and suggests a preliminary hydrogen-bonded Michaelis complex before the formation of the covalent complex. Summary of abstract: Fructose-bisphosphate aldolase is an enzyme that catalyzes a reversible reaction that splits the aldol, fructose 1,6-biphosphate into triose phosphates dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. The reverse reaction occurs in the gluoneogensis and the calvin cycle, both of which are anabolic pathways, and the forward reaction occurs in glycolysis, a catabolic pathway. This enzyme is made of mostly alpha helicies and only has a single sub unit. Resolution of X ray data: 2.8 Å Source: Homo sapiens Classification: LYASE Reaction: D-fructose 1,6-biphosphate=glycerone phosphate + D-glyeraldehyde 3-phosphate Function: Plays a key role in glycolysis and gluconeogenesis. In addition, may also function as scaffolding protein (By similarity). Proteopedia Image #1 PDBSum Image #2 PDBe Image 3

2 Ramachrandran plots (#10) PROCHECK summary of Rama Protein Chain(s): 1 chain; 363 residues Chain chosen for the analysis below= A ProMotif data: Secondary structure summary The Ramachrandran plot appears to agree somewhat with our secondary structure summary. We can see the alpha helicies clearly in the plot, which agrees with the structure summary; however, we do not see evidence of the beta sheets in our structure summary, although it s clearly evident in the Ramchrandran plot. It might be listed under the Other category.

3 Wiring Diagram: Domain data: CATH : # of domains= 1

4 N/A N/A Alpha-Beta Barrel N/A N/A Fructose-biphosphate N/A N/A aldolase 1, chloroplastic Ligands: Ligand highlighted 2FP Ligand 2FP - 1,6-Fructose diphosphate (linear form) Formula: C6H14O12P2 Ligands 2FP 2FP 364(A)

5 Metal ions: N/A Interaction image from ligands: N/A Primary sequence in FASTA format: N/A FASTA homology data 1. Initial result data >4ald:A PYQYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGG VILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAK WRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDH HIYLEGTLLKPNMVTPGHACTQKFSHEEIAMATVTALRRTVPPAVTGITFLSGGQSEEEASINLNAINKCPLLK PWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGQAGAAASESLFVSNHAY

6 2. Data by Residue type #onleft(inblack) %-tage identity PDB code Protein name # % 1ald:A Activity and specificity of human aldolases # % 1ex5:A Fructose 1,6-bisphosphate aldolase from rabbit muscle # % 2ot0:A Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with naphthol as-e phosphate, a competitive inhibitor # % 5tlw:A Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor 1-phosphatebenzene 4-bisphosphonate # % 5tlz:A Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor naphthalene 2,6-bisphosphate # % 1j4e:A Fructose-1,6-bisphosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate Deductions from SAS homology data: Based on the SAS homology search, it appears that the vast majority of the alighned sequences belong to mammals; those listed were humans and rabbits. The difference between human and rabbit aldolase appears to be extremely small; the greatest difference in our listed data was 3.6%. All of the similar proteins appear to be associated with energy storage and production in muscles through the glyconeogenesis and glycolysis pathways.

7 data Functional Enzyme Parameters: KM overall range= -4 to 2 Most common range -2 to -1 Kcat/KM overall range= -2 to 4 Most common range 0 to 1 pi overall range= 5 to 8 Most common range 5 to 6 Turnover # overall range= -6 to 2 Most common range 0 to 1 ph overall range= 5 to 10 Most common range 7 to 8 Temperature overall range= 25 to 80 Most common ran: 35 to 40 & 50 to 55 (#21) Enzyme Class: Lyases; Carbon-carbon lyases; Aldehyde-lyases Comment: Also acts on (3S,4R)-ketose 1-phosphates. The yeast and bacterial enzymes are zinc proteins. The enzymes increase electron-attraction by the carbonyl group, some (Class I) forming a protonated imine with it, others (Class II), mainly of microbial origin, polarizing it with a metal ion, e.g. zinc. Pathway:

8 Reaction catalysed by enzyme: Splits the aldol, fructose 1,6-biphosphate into triose phosphates dihydroxyacetone phosphate and glyceraldehyde 3-phosphate in glycolysis. The reverse reaction occurs in the gluoneogensis and the calvin cycle. Associated disease: Name: Glycogen Storage Diseases Description- Glycogen storage disease (GSD) is an autosomal recessive (all types except IXa and IXd) or X-linked (types IXa and IXd) disorder with symptoms ranging from weakness to growth abnormalities. GSD is caused by a defect in an enzyme gene or a transporter gene involved in glycogen metabolism; types I, VII, and XI for processing of glucose, types II-VI and

9 IX for processing of glycogen, and type 0 for glycogen synthesis. Pompe disease (type II) is a lysosomal storage disease. Category- Inherited metabolic disease Parent Class:EC-Numbers 4 -- Lyases Carbon-carbon lyases Aldehydelyases Systematic Name: D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase (glycerone-phosphate-forming) Summary: Also acts on (3S,4R)-ketose 1-phosphates. The yeast and bacterial enzymes are zinc proteins. The enzymes increase electron-attraction by the carbonyl group, some (Class I) forming a protonated imine with it, others (Class II), mainly of microbial origin, polarizing it with a metal ion, e.g. zinc. Other searches for associated diseases Proteopedia- Glycogen storage disease type 12; caused by a metabolic disorder that is associated with increased hepatic glycogen and hemolytic anemia. All diseases influenced by Fructose-bisphosphate aldolase seem to have to do with glycogen storage and production. RasMol images and analysis Images of overall protein Display:cartoonColours:Grou p Display:cartoonColours:Structur e Display:RibbonsColours: Temp Images of active site Images with AA residues and ligands shown

10 Legend for the 3 images above ALA/A(31)Red ASP/A(33)Blue SER/A(38)Yellow Executive Summary and analysis Fructose-bisphosphate aldolase is an enzyme that catalyzes a reversible reaction that splits the aldol, fructose 1,6-biphosphate into triose phosphates dihydroxyacetone phosphate and glyceraldehyde 3-phosphate in glycolysis. The reverse reaction occurs in the gluoneogensis and the calvin cycle, both of which are anabolic pathways, and the forward reaction occurs in glycolysis, a catabolic pathway. This enzyme is made of mostly alpha helicies and only has a single sub unit. 4ALD is made up of both alpha helicies and beta sheets, both make up 40 and 42 percent respectively. There is only one domain in Fructose-bisphosphate aldolase, an Alpha-Beta Barrel that emphasizes the alpha/beta structures we see in the ramchadaran plot. There were several AA s in active sites on our protien. Per the wiring diagram we see the AC1 blue triangles in several areas, pictured in my above RASMOL I ve emphacised the first area that we see an active site. 31, and 38 are just active sites, but 38 is a catalytic residue in an active site. This makes sense because its ASP, which is an acidic amino acid and is a great producer of hydroxide ions. It s interesting to see how many diseases that a mutation in 4ALD can effect. We see everything from Acidosis, due to a possible stress inducer of a fatal syndrom of aldolase deficiency, to Vitamin E deficency, due to alterations in tissue and serum, per BRENDA s website.