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1y07

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[[Image:1y07.gif|left|200px]]
 
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{{Structure
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==Crystal structure of the superoxide reductase from Treponema pallidum==
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|PDB= 1y07 |SIZE=350|CAPTION= <scene name='initialview01'>1y07</scene>, resolution 1.55&Aring;
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<StructureSection load='1y07' size='340' side='right'caption='[[1y07]], [[Resolution|resolution]] 1.55&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>
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<table><tr><td colspan='2'>[[1y07]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Treponema_pallidum_subsp._pallidum_str._Nichols Treponema pallidum subsp. pallidum str. Nichols]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y07 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y07 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_reductase Superoxide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.2 1.15.1.2] </span>
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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]] 1.55&#8491;</td></tr>
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|GENE= TP0823 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243276 Treponema pallidum subsp. pallidum str. Nichols])
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<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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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|DOMAIN=
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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=1y07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y07 OCA], [https://pdbe.org/1y07 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y07 RCSB], [https://www.ebi.ac.uk/pdbsum/1y07 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y07 ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y07 OCA], [http://www.ebi.ac.uk/pdbsum/1y07 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1y07 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/O83795_TREPA O83795_TREPA]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y0/1y07_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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=1y07 ConSurf].
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<div style="clear:both"></div>
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'''Crystal structure of the superoxide reductase from Treponema pallidum'''
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==See Also==
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*[[Superoxide Reductase|Superoxide Reductase]]
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__TOC__
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==Overview==
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</StructureSection>
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Superoxide reductase (SOR) is a metalloprotein containing a non-heme iron centre, responsible for the scavenging of superoxide radicals in the cell. The crystal structure of Treponema pallidum (Tp) SOR was determined using soft X-rays and synchrotron radiation. Crystals of the oxidized form were obtained using poly(ethylene glycol) and MgCl2 and diffracted beyond 1.55 A resolution. The overall architecture is very similar to that of other known SORs but TpSOR contains an N-terminal domain in which the desulforedoxin-type Fe centre, found in other SORs, is absent. This domain conserves the beta-barrel topology with an overall arrangement very similar to that of other SOR proteins where the centre is present. The absence of the iron ion and its ligands, however, causes a decrease in the cohesion of the domain and some disorder is observed, particularly in the region where the metal would be harboured. The C-terminal domain exhibits the characteristic immunoglobulin-like fold and harbours the Fe(His)4(Cys) active site. The five ligands of the iron centre are well conserved despite some disorder observed for one of the four molecules in the asymmetric unit. The participation of a glutamate as the sixth ligand of some of the iron centres in Pyrococcus furiosus SOR was not observed in TpSOR. A possible explanation is that either X-ray photoreduction occurred or there was a mixture of redox states at the start of data collection. In agreement with earlier proposals, details in the TpSOR structure also suggest that Lys49 might be involved in attraction of superoxide to the active site.
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[[Category: Large Structures]]
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[[Category: Treponema pallidum subsp. pallidum str. Nichols]]
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==About this Structure==
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[[Category: Auchere F]]
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1Y07 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Treponema_pallidum_subsp._pallidum_str._nichols Treponema pallidum subsp. pallidum str. nichols]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y07 OCA].
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[[Category: Bonifacio C]]
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[[Category: Carvalho AL]]
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==Reference==
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[[Category: Moura J]]
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The first crystal structure of class III superoxide reductase from Treponema pallidum., Santos-Silva T, Trincao J, Carvalho AL, Bonifacio C, Auchere F, Raleiras P, Moura I, Moura JJ, Romao MJ, J Biol Inorg Chem. 2006 Jul;11(5):548-58. Epub 2006 May 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16791639 16791639]
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[[Category: Romao MJ]]
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[[Category: Single protein]]
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[[Category: Santos-Silva T]]
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[[Category: Superoxide reductase]]
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[[Category: Trincao J]]
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[[Category: Treponema pallidum subsp. pallidum str. nichols]]
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[[Category: Auchere, F.]]
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[[Category: Bonifacio, C.]]
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[[Category: Carvalho, A L.]]
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[[Category: Moura, J.]]
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[[Category: Romao, M J.]]
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[[Category: Santos-Silva, T.]]
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[[Category: Trincao, J.]]
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[[Category: beta-sheet]]
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[[Category: iron binding]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:57:03 2008''
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Current revision

Crystal structure of the superoxide reductase from Treponema pallidum

PDB ID 1y07

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