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<StructureSection load='2rdn' size='340' side='right'caption='[[2rdn]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
<StructureSection load='2rdn' size='340' side='right'caption='[[2rdn]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2rdn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"streptomyces_avermitilis"_burg_et_al._1979 "streptomyces avermitilis" burg et al. 1979]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDN FirstGlance]. <br>
<table><tr><td colspan='2'>[[2rdn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDN FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PL:(1S,3AS,5AR,8AS)-1,7,7-TRIMETHYL-1,2,3,3A,5A,6,7,8-OCTAHYDROCYCLOPENTA[C]PENTALENE-4-CARBOXYLIC+ACID'>1PL</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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]] 1.35&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2rdq|2rdq]], [[2rdr|2rdr]], [[2rds|2rds]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PL:(1S,3AS,5AR,8AS)-1,7,7-TRIMETHYL-1,2,3,3A,5A,6,7,8-OCTAHYDROCYCLOPENTA[C]PENTALENE-4-CARBOXYLIC+ACID'>1PL</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ptlH ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])</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=2rdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdn OCA], [https://pdbe.org/2rdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdn RCSB], [https://www.ebi.ac.uk/pdbsum/2rdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdn ProSAT]</span></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=2rdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdn OCA], [https://pdbe.org/2rdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdn RCSB], [https://www.ebi.ac.uk/pdbsum/2rdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdn ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PTLH_STRAW PTLH_STRAW]] Catalyzes the conversion of 1-deoxypentalenic acid to 11-beta-hydroxy-1-deoxypentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:16704250</ref> <ref>PMID:17942405</ref>
[https://www.uniprot.org/uniprot/PTLH_STRAW PTLH_STRAW] Catalyzes the conversion of 1-deoxypentalenic acid to 11-beta-hydroxy-1-deoxypentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:16704250</ref> <ref>PMID:17942405</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2rdn 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=2rdn ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The non-heme iron dioxygenase PtlH from the soil organism Streptomyces avermitilis is a member of the iron(II)/alpha-ketoglutarate-dependent dioxygenase superfamily and catalyzes an essential reaction in the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone. To investigate the structural basis for substrate recognition and catalysis, we have determined the x-ray crystal structure of PtlH in several complexes with the cofactors iron, alpha-ketoglutarate, and the non-reactive enantiomer of the substrate, ent-1-deoxypentalenic acid, in four different crystal forms to up to 1.31 A resolution. The overall structure of PtlH forms a double-stranded barrel helix fold, and the cofactor-binding site for iron and alpha-ketoglutarate is similar to other double-stranded barrel helix fold enzymes. Additional secondary structure elements that contribute to the substrate-binding site in PtlH are not conserved in other double-stranded barrel helix fold enzymes. Binding of the substrate enantiomer induces a reorganization of the monoclinic crystal lattice leading to a disorder-order transition of a C-terminal alpha-helix. The newly formed helix blocks the major access to the active site and effectively traps the bound substrate. Kinetic analysis of wild type and site-directed mutant proteins confirms a critical function of two arginine residues in substrate binding, while simulated docking of the enzymatic reaction product reveals the likely orientation of bound substrate.
Crystal structure of the non-heme iron dioxygenase PtlH in pentalenolactone biosynthesis.,You Z, Omura S, Ikeda H, Cane DE, Jogl G J Biol Chem. 2007 Dec 14;282(50):36552-60. Epub 2007 Oct 16. PMID:17942405<ref>PMID:17942405</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2rdn" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Streptomyces avermitilis burg et al. 1979]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cane, D E]]
[[Category: Streptomyces avermitilis]]
[[Category: Ikeda, H]]
[[Category: Cane DE]]
[[Category: Jogl, G]]
[[Category: Ikeda H]]
[[Category: Omura, S]]
[[Category: Jogl G]]
[[Category: You, Z]]
[[Category: Omura S]]
[[Category: Dioxygenase]]
[[Category: You Z]]
[[Category: Double stranded barrel helix]]
[[Category: Oxidoreductase]]

Latest revision as of 09:21, 21 February 2024

Crystal Structure of PtlH with AKG and ent-1PL bound

2rdn, resolution 1.35Å

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