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2rdn

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[[Image:2rdn.gif|left|200px]]
 
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{{Structure
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==Crystal Structure of PtlH with AKG and ent-1PL bound==
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|PDB= 2rdn |SIZE=350|CAPTION= <scene name='initialview01'>2rdn</scene>, resolution 1.350&Aring;
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<StructureSection load='2rdn' size='340' side='right'caption='[[2rdn]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=AKG:2-OXYGLUTARIC+ACID'>AKG</scene> and <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>
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<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>
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|ACTIVITY=
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</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>
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|GENE= ptlH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])
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<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>
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}}
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<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>
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</table>
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'''Crystal Structure of PtlH with AKG and ent-1PL bound'''
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== Function ==
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[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>
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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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.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rdn_consurf.spt"</scriptWhenChecked>
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2RDN is a [[Single protein]] structure of sequence from [http://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].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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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://www.ncbi.nlm.nih.gov/pubmed/17942405 17942405]
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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].
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[[Category: Single protein]]
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Streptomyces avermitilis]]
[[Category: Streptomyces avermitilis]]
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[[Category: Cane, D E.]]
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[[Category: Cane DE]]
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[[Category: Ikeda, H.]]
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[[Category: Ikeda H]]
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[[Category: Jogl, G.]]
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[[Category: Jogl G]]
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[[Category: Omura, S.]]
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[[Category: Omura S]]
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[[Category: You, Z.]]
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[[Category: You Z]]
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[[Category: 1PL]]
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[[Category: AKG]]
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[[Category: FE]]
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[[Category: MG]]
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[[Category: dioxygenase]]
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[[Category: double stranded barrel helix]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:35:00 2008''
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Current revision

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

PDB ID 2rdn

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