Graphics Gallery

Gale Rhodes
Chemistry Department
University of Southern Maine

Revised 2006/08/02

Learn how to use Swiss-PdbViewer. Work through sections 1-4 of the Swiss-PdbViewer Tutorial.

Topic: Glucose Catabolism

FBP, Mg2+, and ADP in PFK-1 (Convergent Stereo)

Examples:

Some Simple Carbohydrates

To review basics of glucose and glycoside structures, click HERE for a Deep View project file containing models of alpha- and beta-D-glucose, maltose, and cellobiose.

Phosphofructokinase, Complex With Products and Allosteric Effector ADP

Phosphofructokinase (PFK-1) is the pacemaker enzyme of glycolysis. Here is a model of two subunits of the tetrameric enzyme from E. coli: 1PFK.pdb.

At the active sites are the products, fructose-1,6-bisphosphate (FBP) and Mg2+/ADP. The crystallographers attempted to crystallize the enzyme with fructose-1-phosphate and ADP, which should produce an inactive complex. To their surprise, the electron-density map clearly showed FBP instead. They suggest that it formed by reaction with contaminating ATP.

Think About It

  • Two molecules of ADP are bound to each subunit. One ADP is bound adjacent to FBP at the active site. The second ADP is far away from this site. What is the role of the second ADP- binding site?
  • Examine the binding of Mg2+ to all four ADP's in the dimer. Does the ion play the same role in all cases?
  • The PDB file 2PFK.pdb is a model of apo-PFK. Get 2PFK.pdb and and superimpose one subunit of it onto 1PFK. Than explore the conformational differences between the two models.
  • Search the PDB for other PFK models that will illuminate the effects of substrate and effector binding (use PDB SearchLite and search for "phosphofructokinase").

Glyceraldehyde-3-Phosphate Dehydrogenase, NAD Binding Site

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the reversible oxidation of G3P by NAD+. Here is a model of the dimeric GAPDH from E. coli: 1GAD.pdb.

Explore the NAD binding site. Find the catalytic side chain of CYS149 near the nicotinamide ring.

Think About It

  • Display the backbone of the protein and color by secondary structure. What type of structure forms the interface between the subunits?
  • The nicotinamide ring of NAD+ can accept hydride ion on either of its two faces. Enzymes that catalyze this reaction are usually stereospecific for one face or the other. If you view the nicotinamide ring with C-4 at the top and the amide substituent to your right, the top face of the ring is called the A face, and the bottom is the B face. Use SPdbV to determine whether GAPDH would direct addition of hydride ion to the A or the B face.
  • The N313T site-directed mutant form of GAPDH exhibits weaker binding of NAD and lower catalytic efficiency. Look at the position of ASN313 with respect to NAD. What kind of interaction occurs between them? What role might ASN313 play in binding and catalysis? If you use SwissPdbViewer, you can compare the mutant with this model. Click here to obtain the coordinate file for the N313T mutant from the Protein Data Bank.

Pyruvate Decarboxylase (Yeast), TPP Binding Site

Pyruvate decarboxylase contains the cofactor thiamine pyrophosphate (TPP). The active form of TPP is the conjugate base, resulting from loss of a proton from C-2, the carbon between N and S in the thiazole ring. Here is a model of the dimeric enzyme from yeast: 1PVD.pdb.

Like many di- and tri-phosphates, TPP is bound to its enzyme as a complex with Mg2+. Restrict your view to atoms within 7 or 8 angstroms of TPP in chain A to see the binding site for TPP. Display the alpha carbons of chains A and B in differenct colors and notice that the TPP binding site includes residues from both subunits. The active sites in this dimer lie at the subunit interfaces.

Think About It

  • Can you find a nearby group that might be responsible for deprotonating C-2 of TPP? What interactions position this group for its role?
  • What might be the role of the pyrophosphate/Mg2+ moiety of TPP?
  • Would you expect a plot of rate versus substrate concentration for this enzyme to exhibit square hyperbola or sigmoid shape?

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