Abstract

This revised application requests funds to continue studies of separate site catalysis by the enzyme pyruvate phosphate dikinase (PPDK). PPDK catalyzes the interconversion of ATP, Pi, and pyruvate with AMP, PPi and PEP by using two separate active sites linked by a carrier histidine residue. The overall goal of the proposed studies is to determine the mechanism by which the carrier histidine is transferred between active sites through precisely oriented and timed domain-domain docking steps. These studies will provide a deeper understanding of the forces controlling transient protein-protein complex formation in signal transduction pathways and template directed biosynthetic pathways.
Five specific aims are listed. These are (1) determine the X-ray crystal structure of PPDK conformer 2, (2) determine the role of domain linkers in facilitating successful domain-domain docking, (3) determine the role of interactions between domain-domain interface residues in facilitating correct docking orientation and in optimizing residence time, (4) distinguish between a through-solvent-domain-diffusion model and a sliding-domain model and (5) identify the role of the PPDK homologue in Mycobacterium tuberculosis. This last aim will be carried out for the purpose of discovering a novel metabolic pathway operating with in this pathogen, as well as a novel target for drug design.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM036260-15A2
Application #
6472961
Study Section
Biochemistry Study Section (BIO)
Program Officer
Ikeda, Richard A
Project Start
1986-01-01
Project End
2006-03-31
Budget Start
2002-04-01
Budget End
2003-03-31
Support Year
15
Fiscal Year
2002
Total Cost
$250,000
Indirect Cost

  Institution

Name
University of New Mexico
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
829868723
City
Albuquerque
State
NM
Country
United States
Zip Code
87131

  Publications

Wu, Chun; Dunaway-Mariano, Debra; Mariano, Patrick S (2013) Design, synthesis, and evaluation of inhibitors of pyruvate phosphate dikinase. J Org Chem 78:1910-22
Reger, Albert S; Wu, Rui; Dunaway-Mariano, Debra et al. (2008) Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase. Biochemistry 47:8016-25
Wu, Rui; Cao, Jian; Lu, Xuefeng et al. (2008) Mechanism of 4-chlorobenzoate:coenzyme a ligase catalysis. Biochemistry 47:8026-39
Lim, Kap; Read, Randy J; Chen, Celia C H et al. (2007) Swiveling domain mechanism in pyruvate phosphate dikinase. Biochemistry 46:14845-53
Chen, Celia C H; Han, Ying; Niu, Weiling et al. (2006) Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: new insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily. Biochemistry 45:11491-504
Lin, Ying; Lusin, Jacqueline D; Ye, Dongmei et al. (2006) Examination of the structure, stability, and catalytic potential in the engineered phosphoryl carrier domain of pyruvate phosphate dikinase. Biochemistry 45:1702-11
Teplyakov, Alexey; Liu, Sijiu; Lu, Zhibing et al. (2005) Crystal structure of the petal death protein from carnation flower. Biochemistry 44:16377-84
Liu, Sijiu; Lu, Zhibing; Han, Yin et al. (2005) Crystal structures of 2-methylisocitrate lyase in complex with product and with isocitrate inhibitor provide insight into lyase substrate specificity, catalysis and evolution. Biochemistry 44:2949-62
Liu, Sijiu; Lu, Zhibing; Han, Ying et al. (2004) Conformational flexibility of PEP mutase. Biochemistry 43:4447-53
Herzberg, Osnat; Chen, Celia C H; Liu, Sijiu et al. (2002) Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis. Biochemistry 41:780-7

Showing the most recent 10 out of 33 publications