2jbw
From Proteopedia
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|PDB= 2jbw |SIZE=350|CAPTION= <scene name='initialview01'>2jbw</scene>, resolution 2.10Å | |PDB= 2jbw |SIZE=350|CAPTION= <scene name='initialview01'>2jbw</scene>, resolution 2.10Å | ||
|SITE= <scene name='pdbsite=TRI:Na+Binding+Site+For+Chain+C'>TRI</scene> | |SITE= <scene name='pdbsite=TRI:Na+Binding+Site+For+Chain+C'>TRI</scene> | ||
| - | |LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene> | + | |LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2jbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jbw OCA], [http://www.ebi.ac.uk/pdbsum/2jbw PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2jbw RCSB]</span> | ||
}} | }} | ||
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[[Category: Schleberger, C.]] | [[Category: Schleberger, C.]] | ||
[[Category: Schulz, G E.]] | [[Category: Schulz, G E.]] | ||
| - | [[Category: NA]] | ||
[[Category: alpha/beta hydrolase]] | [[Category: alpha/beta hydrolase]] | ||
[[Category: c-c bond cleavage]] | [[Category: c-c bond cleavage]] | ||
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[[Category: retro- friedel-crafts acylation]] | [[Category: retro- friedel-crafts acylation]] | ||
| - | ''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 03:55:55 2008'' |
Revision as of 00:56, 31 March 2008
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| , resolution 2.10Å | |||||||
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| Sites: | |||||||
| Ligands: | , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THE 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE.
Overview
The enzyme 2,6-dihydroxy-pseudo-oxynicotine hydrolase from the nicotine-degradation pathway of Arthrobacter nicotinovorans was crystallized and the structure was determined by an X-ray diffraction analysis at 2.1 A resolution. The enzyme belongs to the alpha/beta-hydrolase family as derived from the chain-fold and from the presence of a catalytic triad with its oxyanion hole at the common position. This relationship assigns a pocket lined by the catalytic triad as the active center. The asymmetric unit contains two C(2)-symmetric dimer molecules, each adopting a specific conformation. One dimer forms a more spacious active center pocket and the other a smaller one, suggesting an induced-fit. All of the currently established C-C bond cleaving alpha/beta-hydrolases are from bacterial meta-cleavage pathways for the degradation of aromatic compounds and cover their active center with a 40 residue lid placed between two adjacent strands of the beta-sheet. In contrast, the reported enzyme shields its active center with a 110 residue N-terminal domain, which is absent in the meta-cleavage hydrolases. Since neither the substrate nor an analogue could be bound in the crystals, the substrate was modeled into the active center using the oxyanion hole as a geometric constraint. The model was supported by enzymatic activity data of 11 point mutants and by the two dimer conformations suggesting an induced-fit. Moreover, the model assigned a major role for the large N-terminal domain that is specific to the reported enzyme. The proposal is consistent with the known data for the meta-cleavage hydrolases although it differs in that the reaction does not release alkenes but a hetero-aromatic compound in a retro-Friedel-Crafts acylation. Because the hydrolytic water molecule can be assigned to a geometrically suitable site that can be occupied in the presence of the substrate, the catalytic triad may not form a covalent acyl-enzyme intermediate but merely support a direct hydrolysis.
About this Structure
2JBW is a Single protein structure of sequence from Arthrobacter nicotinovorans. Full crystallographic information is available from OCA.
Reference
Structure and action of a C-C bond cleaving alpha/beta-hydrolase involved in nicotine degradation., Schleberger C, Sachelaru P, Brandsch R, Schulz GE, J Mol Biol. 2007 Mar 23;367(2):409-18. Epub 2006 Dec 30. PMID:17275835
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