View source for 5ydp


==Crystal Structure of TetR Family Repressor AlkX from Dietzia sp. Strain DQ12-45-1b Implicated in Biodegradation of n-Alkanes==
<StructureSection load='5ydp' size='340' side='right' caption='[[5ydp]], [[Resolution|resolution]] 3.09&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ydp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dietzia_sp._dq12-45-1b Dietzia sp. dq12-45-1b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YDP FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AlkwR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=912801 Dietzia sp. DQ12-45-1b])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ydp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydp OCA], [http://pdbe.org/5ydp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ydp RCSB], [http://www.ebi.ac.uk/pdbsum/5ydp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydp ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
n-Alkanes are ubiquitous in nature and are widely used by microorganisms as carbon sources. Alkane hydroxylation by alkane monooxygenases is a critical step in the aerobic biodegradation of n-alkanes, which plays important roles in natural alkane attenuation and is used in industrial and environmental applications. The alkane oxidation operon, alkW1-alkX, in an alkane-degrading strain Dietzia sp. DQ12-45-1b, is negatively auto-regulated by the TetR family repressor, AlkX, via a product positive feedback mechanism. To predict the gene regulation mechanism, we determined the 3.1 A crystal structure of an AlkX homodimer in a non-DNA-bound state. The structure showed traceable long electron density deep inside a hydrophobic cavity of each monomer along the long axis of the helix bundle, and further gas chromatography-mass spectrometry analysis of AlkX revealed that it contained the E.coli-derived long-chain fatty acid molecules as ligand. Moreover, an unusual structural feature of AlkX is an extra helix, alpha6' , forming a lid-like structure with alpha6 covering the inducer-binding pocket and occupying the space between the two symmetrical DNA-binding motifs in one dimer, indicating a distinct conformational transition mode in modulating DNA binding. Sequence alignment of AlkX homologs from Dietzia strains showed that the residues involved in DNA and inducer binding are highly conserved, suggesting that the regulation mechanisms of n-alkane hydroxylation is possibly a common characteristic of Dietzia strains.Importance With ubiquitous n-alkanes in nature, many bacteria from terrestrial and aquatic environments have evolved n-alkane oxidation functions. Alkane hydroxylation by alkane monooxygenases is a critical step in the aerobic biodegradation of n-alkanes, which plays important roles in natural alkane attenuation and petroleum-contaminating environment bioremediation. The gene regulation of the most common alkane hydroxylase AlkB has been studied widely in Gram-negative bacteria, but less explored in Gram-positive bacteria. Our previous study showed that the TetR family regulator (TFR), AlkX, negatively auto-regulated the alkane oxidation operon, alkW1-alkX, in a Gram-positive strain Dietzia sp. DQ12-45-1b. As one of the most common transcriptional regulator family in bacteria, the TFR involving in n-alkane metabolism has been reported only recently. In this study, we determined the crystal structure of AlkX, which implies a distinct DNA/ligand binding mode. Our results shed light upon the regulation mechanism of common alkane degradation process in nature.

Crystal structure of the TetR family repressor, AlkX, from Dietzia sp. DQ12-45-1b implicated in biodegradation of n-alkanes.,Liang JL, Gao Y, He Z, Nie Y, Wang M, JiangYang JH, Zhang XC, Shu WS, Wu XL Appl Environ Microbiol. 2017 Aug 18. pii: AEM.01447-17. doi:, 10.1128/AEM.01447-17. PMID:28821550<ref>PMID:28821550</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5ydp" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Dietzia sp. dq12-45-1b]]
[[Category: Gao, Y]]
[[Category: Liang, J L]]
[[Category: Zheng, H]]
[[Category: 10 alfa helice]]
[[Category: Apo-protein]]
[[Category: Gene regulation]]
[[Category: Homodimer]]