4pgk: Difference between revisions

Revision as of 13:01, 1 February 2023

Insights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Bound

Structural highlights

4pgk is a 1 chain structure with sequence from Prochlorococcus marinus str. MIT 9313. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	FE, Y69
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ALDEC_PROMM Catalyzes the decarbonylation of fatty aldehydes to alkanes. Requires the presence of ferredoxin, ferredoxin reductase and NADPH for in vitro decarbonylase activity (By similarity). Involved in the biosynthesis of alkanes, mainly heptadecane and pentadecane.^[1]

Publication Abstract from PubMed

The nonheme diiron enzyme cyanobacterial aldehyde deformylating oxygenase, cADO, catalyzes the highly unusual deformylation of aliphatic aldehydes to alkanes and formate. We have determined crystal structures for the enzyme with a long-chain water-soluble aldehyde and medium-chain carboxylic acid bound to the active site. These structures delineate a hydrophobic channel that connects the solvent with the deeply buried active site and reveal a mode of substrate binding that is different from previously determined structures with long-chain fatty acids bound. The structures also identify a water channel leading to the active site that could facilitate the entry of protons required in the reaction. NMR studies examining 1-[13C]-octanal binding to cADO indicate that the enzyme binds the aldehyde form rather than the hydrated form. Lastly, the fortuitous cocrystallization of the metal-free form of the protein with aldehyde bound has revealed protein conformation changes that are involved in binding iron.

Insights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Bound.,Buer BC, Paul B, Das D, Stuckey JA, Marsh EN ACS Chem Biol. 2014 Sep 15. PMID:25222710^[2]

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

References

↑ Schirmer A, Rude MA, Li X, Popova E, del Cardayre SB. Microbial biosynthesis of alkanes. Science. 2010 Jul 30;329(5991):559-62. doi: 10.1126/science.1187936. PMID:20671186 doi:10.1126/science.1187936
↑ Buer BC, Paul B, Das D, Stuckey JA, Marsh EN. Insights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Bound. ACS Chem Biol. 2014 Sep 15. PMID:25222710 doi:https://dx.doi.org/10.1021/cb500343j

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OCA

[1] Schirmer A, Rude MA, Li X, Popova E, del Cardayre SB. Microbial biosynthesis of alkanes. Science. 2010 Jul 30;329(5991):559-62. doi: 10.1126/science.1187936. PMID:20671186 doi:10.1126/science.1187936

[2] Buer BC, Paul B, Das D, Stuckey JA, Marsh EN. Insights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Bound. ACS Chem Biol. 2014 Sep 15. PMID:25222710 doi:https://dx.doi.org/10.1021/cb500343j

[1]

[2]

@@ Line 1: / Line 1: @@
 ==Insights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Bound==
-<StructureSection load='4pgk' size='340' side='right' caption='[[4pgk]], [[Resolution|resolution]] 2.17&Aring;' scene=''>
+<StructureSection load='4pgk' size='340' side='right'caption='[[4pgk]], [[Resolution|resolution]] 2.17&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4pgk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Promm Promm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PGK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4pgk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Prochlorococcus_marinus_str._MIT_9313 Prochlorococcus marinus str. MIT 9313]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PGK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=Y69:11-[2-(2-ETHOXYETHOXY)ETHOXY]UNDECANAL'>Y69</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=Y69:11-[2-(2-ETHOXYETHOXY)ETHOXY]UNDECANAL'>Y69</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PMT_1231 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=74547 PROMM])</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=4pgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pgk OCA], [https://pdbe.org/4pgk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pgk RCSB], [https://www.ebi.ac.uk/pdbsum/4pgk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pgk ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Octadecanal_decarbonylase Octadecanal decarbonylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.5 4.1.99.5] </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=4pgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pgk OCA], [http://pdbe.org/4pgk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pgk RCSB], [http://www.ebi.ac.uk/pdbsum/4pgk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pgk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ALDEC_PROMM ALDEC_PROMM]] Catalyzes the decarbonylation of fatty aldehydes to alkanes. Requires the presence of ferredoxin, ferredoxin reductase and NADPH for in vitro decarbonylase activity (By similarity). Involved in the biosynthesis of alkanes, mainly heptadecane and pentadecane.<ref>PMID:20671186</ref>
+[https://www.uniprot.org/uniprot/ALDEC_PROMM ALDEC_PROMM] Catalyzes the decarbonylation of fatty aldehydes to alkanes. Requires the presence of ferredoxin, ferredoxin reductase and NADPH for in vitro decarbonylase activity (By similarity). Involved in the biosynthesis of alkanes, mainly heptadecane and pentadecane.<ref>PMID:20671186</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Octadecanal decarbonylase]]
+[[Category: Large Structures]]
-[[Category: Promm]]
+[[Category: Prochlorococcus marinus str. MIT 9313]]
-[[Category: Buer, B C]]
+[[Category: Buer BC]]
-[[Category: Das, D]]
+[[Category: Das D]]
-[[Category: Marsh, E N.G]]
+[[Category: Marsh ENG]]
-[[Category: Paul, B]]
+[[Category: Paul B]]
-[[Category: Stuckey, J A]]
+[[Category: Stuckey JA]]
-[[Category: Alpha-helix]]
-[[Category: Hydrocarbon production]]
-[[Category: Non-heme di-iron protein]]
-[[Category: Oxidoreductase]]

4pgk: Difference between revisions

Revision as of 13:01, 1 February 2023

Insights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Bound

Structural highlights

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Publication Abstract from PubMed

References

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