1KM5

Crystal structure of ODCase mutant D75N complexed with 6-azaUMP

Summary for 1KM5

• Entry DOI: 10.2210/pdb1km5/pdb
• Related: 1KLY 1KLZ 1KM0 1KM1 1KM2 1KM3 1KM4 1KM6
• Descriptor: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE, CHLORIDE ION, 6-AZA URIDINE 5'-MONOPHOSPHATE, ... (4 entities in total)
• Functional Keywords: tim barrel, lyase
• Biological source: Methanothermobacter thermautotrophicus
• Total number of polymer chains: 1
• Total formula weight: 27155.49

Authors

Wu, N.,Gillon, W.,Pai, E.F. (deposition date: 2001-12-13, release date: 2002-06-28, Last modification date: 2024-02-14)

Primary citation

Wu, N.,Gillon, W.,Pai, E.F.
Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography.
Biochemistry, 41:4002-4011, 2002

PubMed Abstract: The crystal structures of orotidine 5'-monophosphate decarboxylases from four different sources have been published recently. However, the detailed mechanism of catalysis of the most proficient enzyme known to date remains elusive. As the ligand-protein interactions at the orotate binding site are crucial to the understanding of this enzyme, we mutated several of the residues surrounding the aromatic part of the substrate, individually and in combination. The ensuing effects on enzyme structure and stability were characterized by X-ray crystallography of inhibitor, product, or substrate complexes and by chemical denaturation with guanidine hydrochloride, respectively. The results are consistent with the residues K42D70K72D75B being charged and forming an 'alternate charge network' around the reactive part of the substrate. In addition to exerting charge-charge repulsion on the orotate carboxylate, Asp70 also makes a crucial contribution to enzyme stability. Consequently, orotidine 5'-monophosphate decarboxylases seem to require the presence of a negative charge at this position for catalysis as well as for correct and stable folding.

PubMed: 11900543
DOI: 10.1021/bi015758p

Experimental method

X-RAY DIFFRACTION (1.5 Å)