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1knf
From Proteopedia
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| - | [[Image:1knf.gif|left|200px]] | + | [[Image:1knf.gif|left|200px]] |
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| - | '''Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 3-methyl Catechol under Anaerobic Condition''' | + | {{Structure |
| + | |PDB= 1knf |SIZE=350|CAPTION= <scene name='initialview01'>1knf</scene>, resolution 1.9Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MBD:3-METHYLCATECHOL'>MBD</scene> and <scene name='pdbligand=TBU:TERTIARY-BUTYL ALCOHOL'>TBU</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] | ||
| + | |GENE= BPHC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=292 Burkholderia cepacia]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 3-methyl Catechol under Anaerobic Condition''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1KNF is a [ | + | 1KNF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KNF OCA]. |
==Reference== | ==Reference== | ||
| - | Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol., Vaillancourt FH, Han S, Fortin PD, Bolin JT, Eltis LD, J Biol Chem. 1998 Dec 25;273(52):34887-95. PMID:[http:// | + | Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol., Vaillancourt FH, Han S, Fortin PD, Bolin JT, Eltis LD, J Biol Chem. 1998 Dec 25;273(52):34887-95. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9857017 9857017] |
[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]] | [[Category: Biphenyl-2,3-diol 1,2-dioxygenase]] | ||
[[Category: Burkholderia cepacia]] | [[Category: Burkholderia cepacia]] | ||
| Line 25: | Line 34: | ||
[[Category: oxidoreductase]] | [[Category: oxidoreductase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:19:43 2008'' |
Revision as of 10:19, 20 March 2008
| |||||||
| , resolution 1.9Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Gene: | BPHC (Burkholderia cepacia) | ||||||
| Activity: | Biphenyl-2,3-diol 1,2-dioxygenase, with EC number 1.13.11.39 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 3-methyl Catechol under Anaerobic Condition
Overview
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.
About this Structure
1KNF is a Single protein structure of sequence from Burkholderia cepacia. Full crystallographic information is available from OCA.
Reference
Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol., Vaillancourt FH, Han S, Fortin PD, Bolin JT, Eltis LD, J Biol Chem. 1998 Dec 25;273(52):34887-95. PMID:9857017
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