1e5d: Difference between revisions

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New page: left|200px<br /> <applet load="1e5d" size="450" color="white" frame="true" align="right" spinBox="true" caption="1e5d, resolution 2.50Å" /> '''RUBREDOXIN OXYGEN:O...
 
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[[Image:1e5d.gif|left|200px]]<br />
<applet load="1e5d" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1e5d, resolution 2.50&Aring;" />
'''RUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRIO GIGAS'''<br />


==Overview==
==RUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRIO GIGAS==
Desulfovibrio gigas is a strict anaerobe that contains a, well-characterized metabolic pathway that enables it to survive transient, contacts with oxygen. The terminal enzyme in this pathway, rubredoxin:oxygen oxidoreductase (ROO) reduces oxygen to water in a direct, and safe way. The 2.5 A resolution crystal structure of ROO shows that, each monomer of this homodimeric enzyme consists of a novel combination of, two domains, a flavodoxin-like domain and a Zn-beta-lactamase-like domain, that contains a di-iron center for dioxygen reduction. This is the first, structure of a member of a superfamily of enzymes widespread in strict and, facultative anaerobes, indicating its broad physiological significance.
<StructureSection load='1e5d' size='340' side='right'caption='[[1e5d]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1e5d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E5D 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]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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=1e5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e5d OCA], [https://pdbe.org/1e5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e5d RCSB], [https://www.ebi.ac.uk/pdbsum/1e5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e5d ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ROO_MEGG1 ROO_MEGG1] Catalyzes the four-electron reduction of one oxygen molecule to two water molecules.
== 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/e5/1e5d_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=1e5d ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Desulfovibrio gigas is a strict anaerobe that contains a well-characterized metabolic pathway that enables it to survive transient contacts with oxygen. The terminal enzyme in this pathway, rubredoxin:oxygen oxidoreductase (ROO) reduces oxygen to water in a direct and safe way. The 2.5 A resolution crystal structure of ROO shows that each monomer of this homodimeric enzyme consists of a novel combination of two domains, a flavodoxin-like domain and a Zn-beta-lactamase-like domain that contains a di-iron center for dioxygen reduction. This is the first structure of a member of a superfamily of enzymes widespread in strict and facultative anaerobes, indicating its broad physiological significance.


==About this Structure==
Structure of a dioxygen reduction enzyme from Desulfovibrio gigas.,Frazao C, Silva G, Gomes CM, Matias P, Coelho R, Sieker L, Macedo S, Liu MY, Oliveira S, Teixeira M, Xavier AV, Rodrigues-Pousada C, Carrondo MA, Le Gall J Nat Struct Biol. 2000 Nov;7(11):1041-5. PMID:11062560<ref>PMID:11062560</ref>
1E5D is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]] with FMN, FEO and OXY as [[http://en.wikipedia.org/wiki/ligands ligands]]. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1E5D OCA]].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structure of a dioxygen reduction enzyme from Desulfovibrio gigas., Frazao C, Silva G, Gomes CM, Matias P, Coelho R, Sieker L, Macedo S, Liu MY, Oliveira S, Teixeira M, Xavier AV, Rodrigues-Pousada C, Carrondo MA, Le Gall J, Nat Struct Biol. 2000 Nov;7(11):1041-5. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11062560 11062560]
</div>
[[Category: Desulfovibrio gigas]]
<div class="pdbe-citations 1e5d" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
== References ==
[[Category: Carrondo, M.A.]]
<references/>
[[Category: Coelho, R.]]
__TOC__
[[Category: Frazao, C.]]
</StructureSection>
[[Category: Gall, J.Le.]]
[[Category: Large Structures]]
[[Category: Gomes, C.M.]]
[[Category: Megalodesulfovibrio gigas]]
[[Category: Liu, M.Y.]]
[[Category: Carrondo MA]]
[[Category: Macedo, S.]]
[[Category: Coelho R]]
[[Category: Matias, P.]]
[[Category: Frazao C]]
[[Category: Oliveira, S.]]
[[Category: Gomes CM]]
[[Category: Rodrigues-Pousada, C.]]
[[Category: Le Gall J]]
[[Category: Sieker, L.]]
[[Category: Liu MY]]
[[Category: Silva, G.]]
[[Category: Macedo S]]
[[Category: Teixeira, M.]]
[[Category: Matias P]]
[[Category: Xavier, A.V.]]
[[Category: Oliveira S]]
[[Category: FEO]]
[[Category: Rodrigues-Pousada C]]
[[Category: FMN]]
[[Category: Sieker L]]
[[Category: OXY]]
[[Category: Silva G]]
[[Category: diiron-centre]]
[[Category: Teixeira M]]
[[Category: flavoproteins]]
[[Category: Xavier AV]]
[[Category: lactamase-fold]]
[[Category: oxidoreductase]]
[[Category: oxygenreductase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Oct 29 16:55:18 2007''

Latest revision as of 11:46, 9 May 2024

RUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRIO GIGASRUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRIO GIGAS

Structural highlights

1e5d is a 2 chain structure with sequence from Megalodesulfovibrio gigas. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ROO_MEGG1 Catalyzes the four-electron reduction of one oxygen molecule to two water molecules.

Evolutionary Conservation

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

Publication Abstract from PubMed

Desulfovibrio gigas is a strict anaerobe that contains a well-characterized metabolic pathway that enables it to survive transient contacts with oxygen. The terminal enzyme in this pathway, rubredoxin:oxygen oxidoreductase (ROO) reduces oxygen to water in a direct and safe way. The 2.5 A resolution crystal structure of ROO shows that each monomer of this homodimeric enzyme consists of a novel combination of two domains, a flavodoxin-like domain and a Zn-beta-lactamase-like domain that contains a di-iron center for dioxygen reduction. This is the first structure of a member of a superfamily of enzymes widespread in strict and facultative anaerobes, indicating its broad physiological significance.

Structure of a dioxygen reduction enzyme from Desulfovibrio gigas.,Frazao C, Silva G, Gomes CM, Matias P, Coelho R, Sieker L, Macedo S, Liu MY, Oliveira S, Teixeira M, Xavier AV, Rodrigues-Pousada C, Carrondo MA, Le Gall J Nat Struct Biol. 2000 Nov;7(11):1041-5. PMID:11062560[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Frazao C, Silva G, Gomes CM, Matias P, Coelho R, Sieker L, Macedo S, Liu MY, Oliveira S, Teixeira M, Xavier AV, Rodrigues-Pousada C, Carrondo MA, Le Gall J. Structure of a dioxygen reduction enzyme from Desulfovibrio gigas. Nat Struct Biol. 2000 Nov;7(11):1041-5. PMID:11062560 doi:10.1038/80961

1e5d, resolution 2.50Å

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