3b9o: Difference between revisions

Latest revision as of 14:42, 1 November 2023

long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN

Structural highlights

3b9o 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 1.9Å
Ligands:	FMN
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

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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

[2] 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

[3] 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]

[2]

[3]

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3b9o.png|left|200px]]
-<!--
+==long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN==
-The line below this paragraph, containing "STRUCTURE_3b9o", creates the "Structure Box" on the page.
+<StructureSection load='3b9o' size='340' side='right'caption='[[3b9o]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3b9o]] 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=3B9O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B9O FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-{{STRUCTURE_3b9o|  PDB=3b9o  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b9o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b9o OCA], [https://pdbe.org/3b9o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b9o RCSB], [https://www.ebi.ac.uk/pdbsum/3b9o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b9o ProSAT]</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/b9/3b9o_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/main_output.php?pdb_ID=3b9o ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== 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.
-===long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN===
+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<ref>PMID:18164311</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18164311}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3b9o" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18164311 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18164311}}
+__TOC__
+</StructureSection>
-==About this Structure==
-B9O is a 2 chains structure of sequences 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=3B9O OCA].
-==Reference==
-<ref group="xtra">PMID:18164311</ref><references group="xtra"/>
 [[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: Crystal structure]]
-[[Category: Geobacillus thermodenitrifican]]
-[[Category: Lada]]
-[[Category: Monooxygenase]]
-[[Category: Oxidoreductase]]
-[[Category: Plasmid]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 02:33:07 2009''

3b9o: Difference between revisions

Latest revision as of 14:42, 1 November 2023

long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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