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3b9n

From Proteopedia

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Crystal structure of long-chain alkane monooxygenase (LadA)

Structural highlights

3b9n is a 2 chain structure with sequence from Geobacillus thermodenitrificans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LADA_GEOTN Involved in the degradation of long-chain alkanes (PubMed:17372208, PubMed:22526792). Converts alkanes ranging from C(15) to C(36) into their corresponding primary alcohols (PubMed:17372208).^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

LadA, a long-chain alkane monooxygenase, utilizes a terminal oxidation pathway for the conversion of long-chain alkanes (up to at least C(36)) to corresponding primary alcohols in thermophilic bacillus Geobacillus thermodenitrificans NG80-2. Here, we report the first structure of the long-chain alkane hydroxylase, LadA, and its complex with the flavin mononucleotide (FMN) coenzyme. LadA is characterized as a new member of the SsuD subfamily of the bacterial luciferase family via a surprising structural relationship. The LadA:FMN binary complex structure and a LadA:FMN:alkane model reveal a hydrophobic cavity that has dual roles: to provide a hydrogen-bond donor (His138) for catalysis and to create a solvent-free environment in which to stabilize the C4a-hydroperoxyflavin intermediate. Consequently, LadA should catalyze the conversion of long-chain alkanes via the acknowledged flavoprotein monooxygenase mechanism. This finding suggests that the ability of LadA to catalyze the degradation of long-chain alkanes is determined by the binding mode of the long-chain alkane substrates. The LadA structure opens a rational perspective to explore and alter the substrate binding site of LadA, with potential biotechnological applications in areas such as petroleum exploration and treatment of environmental oil pollution.

Crystal structure of long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN: unveiling the long-chain alkane hydroxylase.,Li L, Liu X, Yang W, Xu F, Wang W, Feng L, Bartlam M, Wang L, Rao Z J Mol Biol. 2008 Feb 15;376(2):453-65. Epub 2007 Nov 28. PMID:18164311^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Feng L, Wang W, Cheng J, Ren Y, Zhao G, Gao C, Tang Y, Liu X, Han W, Peng X, Liu R, Wang L. Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5602-7. PMID:17372208 doi:10.1073/pnas.0609650104
↑ Dong Y, Yan J, Du H, Chen M, Ma T, Feng L. Engineering of LadA for enhanced hexadecane oxidation using random site-directed mutagenesis. Appl Microbiol Biotechnol. 2012 May;94(4):1019-29. PMID:22526792 doi:10.1007/s00253-012-4035-y
↑ Li L, Liu X, Yang W, Xu F, Wang W, Feng L, Bartlam M, Wang L, Rao Z. Crystal structure of long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN: unveiling the long-chain alkane hydroxylase. J Mol Biol. 2008 Feb 15;376(2):453-65. Epub 2007 Nov 28. PMID:18164311 doi:10.1016/j.jmb.2007.11.069

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3b9n"

@@ Line 1: / Line 1: @@
 ==Crystal structure of long-chain alkane monooxygenase (LadA)==
-<StructureSection load='3b9n' size='340' side='right' caption='[[3b9n]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='3b9n' size='340' side='right'caption='[[3b9n]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3b9n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans Geobacillus thermodenitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B9N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B9N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3b9n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans Geobacillus thermodenitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B9N FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3b9o|3b9o]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ladA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33940 Geobacillus thermodenitrificans])</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=3b9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b9n OCA], [https://pdbe.org/3b9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b9n RCSB], [https://www.ebi.ac.uk/pdbsum/3b9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b9n ProSAT]</span></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=3b9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b9n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b9n RCSB], [http://www.ebi.ac.uk/pdbsum/3b9n PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LADA_GEOTN LADA_GEOTN] Involved in the degradation of long-chain alkanes (PubMed:17372208, PubMed:22526792). Converts alkanes ranging from C(15) to C(36) into their corresponding primary alcohols (PubMed:17372208).<ref>PMID:17372208</ref> <ref>PMID:22526792</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/b9/3b9n_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b9/3b9n_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3b9n ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3b9n" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 30: / Line 33: @@
 </StructureSection>
 [[Category: Geobacillus thermodenitrificans]]
-[[Category: Bartlam, M]]
+[[Category: Large Structures]]
-[[Category: Li, L]]
+[[Category: Bartlam M]]
-[[Category: Rao, Z]]
+[[Category: Li L]]
-[[Category: Xu, F]]
+[[Category: Rao Z]]
-[[Category: Yang, W]]
+[[Category: Xu F]]
-[[Category: Alkane hydroxylase]]
+[[Category: Yang W]]
-[[Category: Geobacillus thermodenitrifican]]
-[[Category: Lada]]
-[[Category: Monooxygenase]]
-[[Category: Oxidoreductase]]

3b9n

From Proteopedia

Current revision

Crystal structure of long-chain alkane monooxygenase (LadA)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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