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[[Image:2rdn.gif|left|200px]]<br /><applet load="2rdn" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2rdn, resolution 1.350&Aring;" />
'''Crystal Structure of PtlH with AKG and ent-1PL bound'''<br />


==Overview==
==Crystal Structure of PtlH with AKG and ent-1PL bound==
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.
<StructureSection load='2rdn' size='340' side='right'caption='[[2rdn]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<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>
2RDN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis] with <scene name='pdbligand=FE:'>FE</scene>, <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=AKG:'>AKG</scene> and <scene name='pdbligand=1PL:'>1PL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDN OCA].  
</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='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>
==Reference==
<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>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17942405 17942405]
</table>
[[Category: Single protein]]
== 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>
== 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/rd/2rdn_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=2rdn ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Streptomyces avermitilis]]
[[Category: Streptomyces avermitilis]]
[[Category: Cane, D E.]]
[[Category: Cane DE]]
[[Category: Ikeda, H.]]
[[Category: Ikeda H]]
[[Category: Jogl, G.]]
[[Category: Jogl G]]
[[Category: Omura, S.]]
[[Category: Omura S]]
[[Category: You, Z.]]
[[Category: You Z]]
[[Category: 1PL]]
[[Category: AKG]]
[[Category: FE]]
[[Category: MG]]
[[Category: dioxygenase]]
[[Category: double stranded barrel helix]]
[[Category: oxidoreductase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:46:28 2008''

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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