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| | {{STRUCTURE_1iwb| PDB=1iwb | SCENE= }} | | {{STRUCTURE_1iwb| PDB=1iwb | SCENE= }} |
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| - | '''Crystal structure of diol dehydratase'''
| + | ===Crystal structure of diol dehydratase=== |
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| - | ==Overview==
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| - | 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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_12379103}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 12379103 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_12379103}} |
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| | ==About this Structure== | | ==About this Structure== |
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| | [[Category: Yasuoka, N.]] | | [[Category: Yasuoka, N.]] |
| | [[Category: Beta-alpha-barrel]] | | [[Category: Beta-alpha-barrel]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 20:30:05 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 14:07:13 2008'' |
Revision as of 11:07, 1 July 2008
Template:STRUCTURE 1iwb
Crystal structure of diol dehydratase
Template:ABSTRACT PUBMED 12379103
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
Page seeded by OCA on Tue Jul 1 14:07:13 2008
