1iwb
From Proteopedia
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| - | [[Image:1iwb.jpg|left|200px]] | + | [[Image:1iwb.jpg|left|200px]] |
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| - | '''Crystal structure of diol dehydratase''' | + | {{Structure |
| + | |PDB= 1iwb |SIZE=350|CAPTION= <scene name='initialview01'>1iwb</scene>, resolution 1.85Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=K:POTASSIUM+ION'>K</scene> and <scene name='pdbligand=B12:COBALAMIN'>B12</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Propanediol_dehydratase Propanediol dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.28 4.2.1.28] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''Crystal structure of diol dehydratase''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1IWB is a [ | + | 1IWB is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IWB OCA]. |
==Reference== | ==Reference== | ||
| - | Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase., Shibata N, Masuda J, Morimoto Y, Yasuoka N, Toraya T, Biochemistry. 2002 Oct 22;41(42):12607-17. PMID:[http:// | + | Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase., Shibata N, Masuda J, Morimoto Y, Yasuoka N, Toraya T, Biochemistry. 2002 Oct 22;41(42):12607-17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12379103 12379103] |
[[Category: Klebsiella oxytoca]] | [[Category: Klebsiella oxytoca]] | ||
[[Category: Propanediol dehydratase]] | [[Category: Propanediol dehydratase]] | ||
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[[Category: B12]] | [[Category: B12]] | ||
[[Category: K]] | [[Category: K]] | ||
| - | [[Category: beta-alpha- | + | [[Category: beta-alpha-barrel]] |
| - | ''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 11:55:46 2008'' |
Revision as of 09:55, 20 March 2008
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| , resolution 1.85Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Activity: | Propanediol dehydratase, with EC number 4.2.1.28 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of diol dehydratase
Overview
Substrate binding triggers catalytic radical formation through the cobalt-carbon bond homolysis in coenzyme B12-dependent enzymes. We have determined the crystal structure of the substrate-free form of Klebsiella oxytoca diol dehydratase*cyanocobalamin complex at 1.85 A resolution. The structure contains two units of the heterotrimer consisting of alpha, beta, and gamma subunits. As compared with the structure of its substrate-bound form, the beta subunits are tilted by approximately 3 degrees and cobalamin is also tilted so that pyrrole rings A and D are significantly lifted up toward the substrate-binding site, whereas pyrrole rings B and C are only slightly lifted up. The structure revealed that the potassium ion in the substrate-binding site of the substrate-free enzyme is also heptacoordinated; that is, two oxygen atoms of two water molecules coordinate to it instead of the substrate hydroxyls. A modeling study in which the structures of both the cobalamin moiety and the adenine ring of the coenzyme were superimposed onto those of the enzyme-bound cyanocobalamin and the adenine ring-binding pocket, respectively, demonstrated that the distortions of the Co-C bond in the substrate-free form are already marked but slightly smaller than those in the substrate-bound form. It was thus strongly suggested that the Co-C bond becomes largely activated (labilized) when the coenzyme binds to the apoenzyme even in the absence of substrate and undergoes homolysis through the substrate-induced conformational changes of the enzyme. Kinetic coupling of Co-C bond homolysis with hydrogen abstraction from the substrate shifts the equilibrium to dissociation.
About this Structure
1IWB is a Protein complex structure of sequences from Klebsiella oxytoca. Full crystallographic information is available from OCA.
Reference
Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase., Shibata N, Masuda J, Morimoto Y, Yasuoka N, Toraya T, Biochemistry. 2002 Oct 22;41(42):12607-17. PMID:12379103
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