Chemistry Department University of Southern Maine
Links To Files Used In Biochemistry Class (CHY 361-363)
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Topic: Bioenergetics and Metabolism
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Molecules to Study
ATP and Other "High-Energy" Phosphates
Crystallographic models of ATP-binding proteins, especially enzymes that catalyze phosphate transfers, often contain ADPNP, a non-hydrolyzable nitrogen analog of ATP. This analog takes the name ANP in PDB files.
Mg2+-ATP Complex
ATP exists commonly in complexes with Mg2+. Here is a model of Mg2+ in complex ADPNP, as found in bovine mitochondrial ATPase (PDB file 1BMF): MgANP.pdb.
Display the structure as a ball and stick model to see how the magnesium ion (green) bridges phosphate oxygens.
Think About It
This is not the only way that Mg2+ is found bound to ATP in proteins. Imagine other ways in which this ion could bridge two negatively charged oxygens in di- or tri-phosphates.
ATP/AMP In Adenylate Kinase
Adenylate kinase catalyzes this reaction: AMP + ATP <=> 2 ADP. This is the first 1st step in returning AMP, produced in adenylate transfers, to the ATP cycle. Here is one chain of the dimeric enzyme (from PDB file 1ANK), with bound ADPNP and AMP, showing how the enzyme brings these two nucleotides together for phosphate transfer: 1ANKChA.pdb.
Use your molecular viewer study the structure of the enzyme, and to explore the binding sites for ATP and AMP.
Think About It
· Can you find structural elements typical of nucleotide-binding proteins? Look for parallel pleated sheets with strands linked by alpha helices. Also look for helices whose dipoles might stabilize the negative charge of phosphates.
· What amino-acid side chains would you expect to be involved in binding phosphates? Can you find any of these amino acids near the phosphate groups of ADPNP and AMP?
Mg2+-ATP/3-phosphoglycerate in Phosphoglycerate Kinase (PGK)
PGK, an enzyme in glycolysis, catalyzes this group-transfer reaction:
1,3-bis-phosphoglycerate + ADP<==> 3-phosphoglycerate + ATP. Here is a complex of PGK with its products, Mg2+ATP and 3-phosphoglycerate (3PG): 3PGK.pdb.
Use your molecular viewer to study the structure of the enzyme, and to explore the binding sites of the products.
Think About It· Can you find structural elements typical of nucleotide-binding proteins?
· In the ATP and 3PG regions, can you find any unrealistic features in this model?
NAD+ Binding Site in Lactate Dehydrogenase (LDH)
LDH catalyzes this reaction: pyruvate + NADH + H+ <==> lactate + NAD+. NAD+ /NADH is frequently the redox couple involved in the interconversion of polar functional groups like the C=O/C-OH group interconversion in this reaction. Here is a model of NAD+ in its LDH binding site: NAD9LDT.pdb.
Think About It
· Compare the NAD-binding domain of LDH with the ATP-binding region of PGK. Do you see any shared features?
· This model includes only the first of two domains in LDH (specifically, residues 19-162). Where on the surface of this domain would you expect the second domain to lie? Think about 1) the location of the reactive portion of NAD in the reaction catalyzed by LDH, and 2) the type of amino acids you would find on the surface of one domain where it is in contact with another domain. To see if your speculation is correct, obtain the file 9LDT from the Protein Data Bank. The second domain comprises residues 163-330.
· How might
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