1KMY

Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 2,3-dihydroxybiphenyl under Anaerobic Condition

Summary for 1KMY

• Entry DOI: 10.2210/pdb1kmy/pdb
• Related: 1HAN 1KND 1KNF
• Descriptor: 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE, FE (II) ION, BIPHENYL-2,3-DIOL, ... (5 entities in total)
• Functional Keywords: dioxygenase, 2, 3-dihydroxybiphenyl, oxidoreductase
• Biological source: Burkholderia xenovorans
• Total number of polymer chains: 1
• Total formula weight: 32693.77

Authors

Han, S.,Bolin, J.T. (deposition date: 2001-12-17, release date: 2002-02-20, Last modification date: 2023-08-16)

Primary citation

Vaillancourt, F.H.,Han, S.,Fortin, P.D.,Bolin, J.T.,Eltis, L.D.
Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol.
J.Biol.Chem., 273:34887-34895, 1998

PubMed Abstract: The steady-state cleavage of catechols by 2,3-dihydroxybiphenyl 1, 2-dioxygenase (DHBD), the extradiol dioxygenase of the biphenyl biodegradation pathway, was investigated using a highly active, anaerobically purified preparation of enzyme. The kinetic data obtained using 2,3-dihydroxybiphenyl (DHB) fit a compulsory order ternary complex mechanism in which substrate inhibition occurs. The Km for dioxygen was 1280 +/- 70 microM, which is at least 2 orders of magnitude higher than that reported for catechol 2,3-dioxygenases. Km and Kd for DHB were 22 +/- 2 and 8 +/- 1 microM, respectively. DHBD was subject to reversible substrate inhibition and mechanism-based inactivation. In air-saturated buffer, the partition ratios of catecholic substrates substituted at C-3 were inversely related to their apparent specificity constants. Small organic molecules that stabilized DHBD most effectively also inhibited the cleavage reaction most strongly. The steady-state kinetic data and crystallographic results suggest that the stabilization and inhibition are due to specific interactions between the organic molecule and the active site of the enzyme. t-Butanol stabilized the enzyme and inhibited the cleavage of DHB in a mixed fashion, consistent with the distinct binding sites occupied by t-butanol in the crystal structures of the substrate-free form of the enzyme and the enzyme-DHB complex. In contrast, crystal structures of complexes with catechol and 3-methylcatechol revealed relationships between the binding of these smaller substrates and t-butanol that are consistent with the observed competitive inhibition.

PubMed: 9857017
DOI: 10.1074/jbc.273.52.34887

Experimental method

X-RAY DIFFRACTION (2 Å)