1uc4
From Proteopedia
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|PDB= 1uc4 |SIZE=350|CAPTION= <scene name='initialview01'>1uc4</scene>, resolution 1.80Å | |PDB= 1uc4 |SIZE=350|CAPTION= <scene name='initialview01'>1uc4</scene>, resolution 1.80Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=CNC:CO-CYANOCOBALAMIN'>CNC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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=[[1uc5|1UC5]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1uc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc4 OCA], [http://www.ebi.ac.uk/pdbsum/1uc4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1uc4 RCSB]</span> | ||
}} | }} | ||
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[[Category: Yamanishi, M.]] | [[Category: Yamanishi, M.]] | ||
[[Category: Yasuoka, N.]] | [[Category: Yasuoka, N.]] | ||
| - | [[Category: CNC]] | ||
| - | [[Category: K]] | ||
| - | [[Category: NH4]] | ||
| - | [[Category: PGO]] | ||
[[Category: alpha/beta barrel]] | [[Category: alpha/beta barrel]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:08:17 2008'' |
Revision as of 21:08, 30 March 2008
| |||||||
| , resolution 1.80Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Activity: | Propanediol dehydratase, with EC number 4.2.1.28 | ||||||
| Related: | 1UC5
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of diol dehydratase complexed with (S)-1,2-propanediol
Overview
Adenosylcobalamin-dependent diol dehydratase of Klebsiella oxytoca is apparently not stereospecific and catalyzes the conversion of both (R)- and (S)-1,2-propanediol to propionaldehyde. To explain this unusual property of the enzyme, we analyzed the crystal structures of diol dehydratase in complexes with cyanocobalamin and (R)- or (S)-1,2-propanediol. (R)- and (S)-isomers are bound in a symmetrical manner, although the hydrogen-bonding interactions between the substrate and the active-site residues are the same. From the position of the adenosyl radical in the modeled "distal" conformation, it is reasonable for the radical to abstract the pro-R and pro-S hydrogens from (R)- and (S)-isomers, respectively. The hydroxyl groups in the substrate radicals would migrates from C(2) to C(1) by a suprafacial shift, resulting in the stereochemical inversion at C(1). This causes 60 degrees clockwise and 70 degrees counterclockwise rotations of the C(1)-C(2) bond of the (R)- and (S)-isomers, respectively, if viewed from K+. A modeling study of 1,1-gem-diol intermediates indicated that new radical center C(2) becomes close to the methyl group of 5'-deoxyadenosine. Thus, the hydrogen back-abstraction (recombination) from 5'-deoxyadenosine by the product radical is structurally feasible. It was also predictable that the substitution of the migrating hydroxyl group by a hydrogen atom from 5'-deoxyadenosine takes place with the inversion of the configuration at C(2) of the substrate. Stereospecific dehydration of the 1,1-gem-diol intermediates can also be rationalized by assuming that Asp-alpha335 and Glu-alpha170 function as base catalysts in the dehydration of the (R)- and (S)-isomers, respectively. The structure-based mechanism and stereochemical courses of the reaction are proposed.
About this Structure
1UC4 is a Protein complex structure of sequences from Klebsiella oxytoca. Full crystallographic information is available from OCA.
Reference
Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase., Shibata N, Nakanishi Y, Fukuoka M, Yamanishi M, Yasuoka N, Toraya T, J Biol Chem. 2003 Jun 20;278(25):22717-25. Epub 2003 Apr 8. PMID:12684496
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