Article

Solution 1H NMR of the active site of substrate-bound, cyanide-inhibited human heme oxygenase. comparison to the crystal structure of the water-ligated form.

University of California, Department of Chemistry, Davis, California 95616, USA.
Journal of Biological Chemistry (impact factor: 4.77). 06/2001; 276(19):15676-87. DOI:10.1074/jbc.M009974200 pp.15676-87
Source: PubMed

ABSTRACT The majority of the active site residues of cyanide-inhibited, substrate-bound human heme oxygenase have been assigned on the basis of two-dimensional NMR using the crystal structure of the water-ligated substrate complex as a guide (Schuller, D. J., Wilks, A., Ortiz de Montellano, P. R., and Poulos, T. L. (1999) Nat. Struct. Biol. 6, 860-867). The proximal helix and the N-terminal portion of the distal helix are found to be identical to those in the crystal except that the heme for the major isomer ( approximately 75-80%) in solution is rotated 180 degrees about the alpha-gamma-meso axis relative to the unique orientation in the crystal. The central portion of the distal helix in solution is translated slightly over the heme toward the distal ligand, and a distal four-ring aromatic cluster has moved 1-2 A closer to the heme, which allows for strong hydrogen bonds between the hydroxyls of Tyr-58 and Tyr-137. These latter interactions are proposed to stabilize the closed pocket conducive to the high stereospecificity of the alpha-meso ring opening. The determination of the magnetic axes, for which the major axis is controlled by the Fe-CN orientation, reveals a approximately 20 degrees tilt of the distal ligand from the heme normal in the direction of the alpha-meso bridge, demonstrating that the close placement of the distal helix over the heme exerts control of stereospecificity by both blocking access to the beta, gamma, and delta-meso positions and tilting the axial ligand, a proposed peroxide, toward the alpha-meso position.

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    Article: Identification of ligand binding sites of proteins using the Gaussian Network Model.
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    ABSTRACT: The nonlocal nature of the protein-ligand binding problem is investigated via the Gaussian Network Model with which the residues lying along interaction pathways in a protein and the residues at the binding site are predicted. The predictions of the binding site residues are verified by using several benchmark systems where the topology of the unbound protein and the bound protein-ligand complex are known. Predictions are made on the unbound protein. Agreement of results with the bound complexes indicates that the information for binding resides in the unbound protein. Cliques that consist of three or more residues that are far apart along the primary structure but are in contact in the folded structure are shown to be important determinants of the binding problem. Comparison with known structures shows that the predictive capability of the method is significant.
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Keywords

20 degrees tilt
 
active site residues
 
alpha-gamma-meso axis
 
alpha-meso bridge
 
alpha-meso position
 
alpha-meso ring opening
 
axial ligand
 
closed pocket conducive
 
crystal structure
 
delta-meso positions
 
distal helix
 
distal ligand
 
heme normal
 
major axis
 
major isomer
 
proximal helix
 
strong hydrogen bonds
 
substrate-bound human heme oxygenase
 
two-dimensional NMR
 
water-ligated substrate complex