1knd
From Proteopedia
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|PDB= 1knd |SIZE=350|CAPTION= <scene name='initialview01'>1knd</scene>, resolution 1.9Å | |PDB= 1knd |SIZE=350|CAPTION= <scene name='initialview01'>1knd</scene>, resolution 1.9Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= BPHC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=292 Burkholderia cepacia]) | |GENE= BPHC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=292 Burkholderia cepacia]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1han|1HAN]], [[1kmy|1KMY]], [[1knf|1KNF]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1knd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1knd OCA], [http://www.ebi.ac.uk/pdbsum/1knd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1knd RCSB]</span> | ||
}} | }} | ||
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[[Category: Bolin, J T.]] | [[Category: Bolin, J T.]] | ||
[[Category: Han, S.]] | [[Category: Han, S.]] | ||
| - | + | [[Category: 2,3-dihydroxybiphenyl]] | |
| - | + | ||
| - | + | ||
| - | [[Category: 2 | + | |
| - | + | ||
[[Category: catechol]] | [[Category: catechol]] | ||
[[Category: dioxygenase]] | [[Category: dioxygenase]] | ||
[[Category: oxidoreductase]] | [[Category: oxidoreductase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:50:56 2008'' |
Revision as of 18:50, 30 March 2008
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| , resolution 1.9Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | BPHC (Burkholderia cepacia) | ||||||
| Activity: | Biphenyl-2,3-diol 1,2-dioxygenase, with EC number 1.13.11.39 | ||||||
| Related: | 1HAN, 1KMY, 1KNF
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 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
1KND 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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