1jyb: Difference between revisions

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New page: left|200px<br /><applet load="1jyb" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jyb, resolution 2.2Å" /> '''Crystal structure of ...
 
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[[Image:1jyb.gif|left|200px]]<br /><applet load="1jyb" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1jyb, resolution 2.2&Aring;" />
'''Crystal structure of Rubrerythrin'''<br />


==Overview==
==Crystal structure of Rubrerythrin==
Rubrerythrin (Rr) is a non-heme iron protein isolated from anaerobic, sulfate-reducing bacteria. Rr is a dimeric molecule, each monomer contains, a Fe(SCys)(4) center in the C-terminal domain and a binuclear metal center, in the N-terminal domain. Rr structures with different protein sources, and/or preparation procedures have been studied. Two Rr crystal structures, have been solved with significant differences in their binuclear metal, centers. The first structure, which was obtained from expressed protein, under aerobic conditions, has a diiron-oxo center. The second structure, which was obtained from native protein of Desulfovibrio vulgaris under, aerobic conditions, has an Fe-Zn center with the zinc position differing, from the corresponding iron position in the former structure by, approximately 2 A. The crystal structures of Rr isolated from D. vulgaris, (Hildenborough, NCIB 8303), the same as the second structured but prepared, under anaerobic conditions, are reported in this paper. The binuclear, metal center in these structures is an Fe-Zn center. When the crystal was, exposed to air, the zinc atom moved gradually, approximately 2 A, accompanied by the entrance of a water molecule (or hydroxyl group) and, changes in the binuclear metal center microenvironment. This finding can, explain the differences between the two different structures. The results, suggest that the zinc movement may be related to the enzymatic activity of, Rr.
<StructureSection load='1jyb' size='340' side='right'caption='[[1jyb]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1jyb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JYB FirstGlance]. <br>
1JYB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with FE and ZN as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JYB 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]] 2.2&#8491;</td></tr>
 
<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=ZN:ZINC+ION'>ZN</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=1jyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jyb OCA], [https://pdbe.org/1jyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jyb RCSB], [https://www.ebi.ac.uk/pdbsum/1jyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jyb ProSAT]</span></td></tr>
Crystal structure studies on rubrerythrin: enzymatic activity in relation to the zinc movement., Li M, Liu MY, LeGall J, Gui LL, Liao J, Jiang T, Zhang JP, Liang DC, Chang WR, J Biol Inorg Chem. 2003 Jan;8(1-2):149-55. Epub 2002 Sep 10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12459910 12459910]
</table>
== Function ==
[https://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).
== 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/jy/1jyb_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=1jyb ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Desulfovibrio vulgaris]]
[[Category: Desulfovibrio vulgaris]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Chang, W.R.]]
[[Category: Chang WR]]
[[Category: Li, M.]]
[[Category: Li M]]
[[Category: Liu, M.Y.]]
[[Category: Liu MY]]
[[Category: FE]]
[[Category: ZN]]
[[Category: alpha helix bundle]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:41:12 2007''

Latest revision as of 16:25, 13 March 2024

Crystal structure of RubrerythrinCrystal structure of Rubrerythrin

Structural highlights

1jyb is a 1 chain structure with sequence from Desulfovibrio vulgaris. 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

RUBY_DESVH May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).

Evolutionary Conservation

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

1jyb, resolution 2.20Å

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