1q0f: Difference between revisions

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New page: left|200px<br /><applet load="1q0f" size="450" color="white" frame="true" align="right" spinBox="true" caption="1q0f, resolution 2.20Å" /> '''Crystal structure of...
 
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[[Image:1q0f.gif|left|200px]]<br /><applet load="1q0f" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1q0f, resolution 2.20&Aring;" />
'''Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the state after partial x-ray-induced reduction'''<br />


==Overview==
==Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the state after partial x-ray-induced reduction==
Superoxide dismutases (SODs, EC 1.15.1.1) are ubiquitous enzymes that, efficiently catalyze the dismutation of superoxide radical anions to, protect biological molecules from oxidative damage. The crystal structure, of nickel-containing SOD (NiSOD) from Streptomyces seoulensis was, determined for the resting, x-ray-reduced, and thiosulfate-reduced enzyme, state. NiSOD is a homohexamer consisting of four-helix-bundle subunits., The catalytic center resides in the N-terminal active-site loop, where a, Ni(III) ion is coordinated by the amino group of His-1, the amide group of, Cys-2, two thiolate groups of Cys-2 and Cys-6, and the imidazolate of, His-1 as axial ligand that is lost in the chemically reduced state as well, as after x-ray-induced reduction. This structure represents a third class, of SODs concerning the catalytic metal species, subunit structure, and, oligomeric organization. It adds a member to the small number of, Ni-metalloenzymes and contributes with its Ni(III) active site to the, general understanding of Ni-related biochemistry. NiSOD is shown to occur, also in bacteria other than Streptomyces and is predicted to be present in, some cyanobacteria.
<StructureSection load='1q0f' size='340' side='right'caption='[[1q0f]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1q0f]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_seoulensis Streptomyces seoulensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q0F FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3NI:NICKEL+(III)+ION'>3NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1q0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0f OCA], [https://pdbe.org/1q0f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q0f RCSB], [https://www.ebi.ac.uk/pdbsum/1q0f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q0f ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SODN_STRSO SODN_STRSO]
== 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/q0/1q0f_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=1q0f ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1Q0F is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_seoulensis Streptomyces seoulensis] with SO4 and 3NI as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Q0F OCA].
*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structure of nickel-containing superoxide dismutase reveals another type of active site., Wuerges J, Lee JW, Yim YI, Yim HS, Kang SO, Carugo KD, Proc Natl Acad Sci U S A. 2004 Jun 8;101(23):8569-74. Epub 2004 Jun 1. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15173586 15173586]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Streptomyces seoulensis]]
[[Category: Streptomyces seoulensis]]
[[Category: Superoxide dismutase]]
[[Category: Djinovic Carugo K]]
[[Category: Carugo, K.Djinovic.]]
[[Category: Kang S-O]]
[[Category: Kang, S.O.]]
[[Category: Lee J-W]]
[[Category: Lee, J.W.]]
[[Category: Wuerges J]]
[[Category: Wuerges, J.]]
[[Category: Yim H-S]]
[[Category: Yim, H.S.]]
[[Category: Yim Y-I]]
[[Category: Yim, Y.I.]]
[[Category: 3NI]]
[[Category: SO4]]
[[Category: homohexamer of four-helix bundles]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:16:45 2007''

Latest revision as of 11:11, 14 February 2024

Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the state after partial x-ray-induced reductionCrystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the state after partial x-ray-induced reduction

Structural highlights

1q0f is a 12 chain structure with sequence from Streptomyces seoulensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SODN_STRSO

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1q0f, resolution 2.20Å

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