2jbw: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| (20 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
== | ==Crystal Structure of the 2,6-dihydroxy-pseudo-oxynicotine Hydrolase.== | ||
The enzyme 2,6-dihydroxy-pseudo-oxynicotine hydrolase from the | <StructureSection load='2jbw' size='340' side='right'caption='[[2jbw]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2jbw]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenarthrobacter_nicotinovorans Paenarthrobacter nicotinovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JBW FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jbw OCA], [https://pdbe.org/2jbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jbw RCSB], [https://www.ebi.ac.uk/pdbsum/2jbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jbw ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DHPON_PAENI DHPON_PAENI] L-nicotine is used as a growth substrate. Plays a role in nicotine catabolism by cleaving a C-C bond in 2,6-dihydroxypseudooxynicotine.<ref>PMID:16321959</ref> <ref>PMID:17275835</ref> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jb/2jbw_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2jbw ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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<ref>PMID:17275835</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 2jbw" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Brandsch | <references/> | ||
[[Category: Sachelaru | __TOC__ | ||
[[Category: Schleberger | </StructureSection> | ||
[[Category: Schulz | [[Category: Large Structures]] | ||
[[Category: Paenarthrobacter nicotinovorans]] | |||
[[Category: Brandsch R]] | |||
[[Category: Sachelaru P]] | |||
[[Category: Schleberger C]] | |||
[[Category: Schulz GE]] | |||
