1eex
From Proteopedia
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|PDB= 1eex |SIZE=350|CAPTION= <scene name='initialview01'>1eex</scene>, resolution 1.7Å | |PDB= 1eex |SIZE=350|CAPTION= <scene name='initialview01'>1eex</scene>, resolution 1.7Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=COY:CO-(ADENIN-9-YL-PENTYL)-COBALAMIN'>COY</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PGO:1,2-PROPANEDIOL'>PGO</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]], [[1egm|1EGM]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1eex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eex OCA], [http://www.ebi.ac.uk/pdbsum/1eex PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1eex RCSB]</span> | ||
}} | }} | ||
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[[Category: Toraya, T.]] | [[Category: Toraya, T.]] | ||
[[Category: Yasuoka, N.]] | [[Category: Yasuoka, N.]] | ||
| - | [[Category: COY]] | ||
| - | [[Category: K]] | ||
| - | [[Category: PGO]] | ||
[[Category: coenzyme b12]] | [[Category: coenzyme b12]] | ||
[[Category: potassium ion]] | [[Category: potassium ion]] | ||
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[[Category: tim barrel]] | [[Category: tim 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 20:01:14 2008'' |
Revision as of 17:01, 30 March 2008
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| , resolution 1.7Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | Propanediol dehydratase, with EC number 4.2.1.28 | ||||||
| Related: | 1DIO, 1EGM
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA
Overview
BACKGROUND: Adenosylcobalamin (coenzyme B(12)) serves as a cofactor for enzymatic radical reactions. The adenosyl radical, a catalytic radical in these reactions, is formed by homolysis of the cobalt-carbon bond of the coenzyme, although the mechanism of cleavage of its organometallic bond remains unsolved. RESULTS: We determined the three-dimensional structures of diol dehydratase complexed with adeninylpentylcobalamin and with cyanocobalamin at 1.7 A and 1.9 A resolution, respectively, at cryogenic temperatures. In the adeninylpentylcobalamin complex, the adenine ring is bound parallel to the corrin ring as in the free form and methylmalonyl-CoA-mutase-bound coenzyme, but with the other side facing pyrrole ring C. All of its nitrogen atoms except for N(9) are hydrogen-bonded to mainchain amide oxygen and amide nitrogen atoms, a sidechain hydroxyl group, and a water molecule. As compared with the cyanocobalamin complex, the sidechain of Seralpha224 rotates by 120 degrees to hydrogen bond with N(3) of the adenine ring. CONCLUSIONS: The structure of the adenine-ring-binding site provides a molecular basis for the strict specificity of diol dehydratase for the coenzyme adenosyl group. The superimposition of the structure of the free coenzyme on that of enzyme-bound adeninylpentylcobalamin demonstrated that the tight enzyme-coenzyme interactions at both the cobalamin moiety and adenine ring of the adenosyl group would inevitably lead to cleavage of the cobalt-carbon bond. Rotation of the ribose moiety around the glycosidic linkage makes the 5'-carbon radical accessible to the hydrogen atom of the substrate to be abstracted.
About this Structure
1EEX is a Protein complex structure of sequences from Klebsiella oxytoca. Full crystallographic information is available from OCA.
Reference
How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex., Masuda J, Shibata N, Morimoto Y, Toraya T, Yasuoka N, Structure. 2000 Jul 15;8(7):775-88. PMID:10903944
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