1iwb
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1iwb |SIZE=350|CAPTION= <scene name='initialview01'>1iwb</scene>, resolution 1.85Å | |PDB= 1iwb |SIZE=350|CAPTION= <scene name='initialview01'>1iwb</scene>, resolution 1.85Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1dio|1DIO]], [[1eex|1EEX]], [[1egm|1EGM]], [[1egv|1EGV]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iwb OCA], [http://www.ebi.ac.uk/pdbsum/1iwb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1iwb RCSB]</span> | ||
}} | }} | ||
| Line 28: | Line 31: | ||
[[Category: Toraya, T.]] | [[Category: Toraya, T.]] | ||
[[Category: Yasuoka, N.]] | [[Category: Yasuoka, N.]] | ||
| - | [[Category: B12]] | ||
| - | [[Category: K]] | ||
[[Category: beta-alpha-barrel]] | [[Category: beta-alpha-barrel]] | ||
| - | ''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 21:25:34 2008'' |
Revision as of 18:25, 30 March 2008
| |||||||
| , resolution 1.85Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Activity: | Propanediol dehydratase, with EC number 4.2.1.28 | ||||||
| Related: | 1DIO, 1EEX, 1EGM, 1EGV
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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
Page seeded by OCA on Sun Mar 30 21:25:34 2008
