1e5d: Difference between revisions

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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 2.50Å" />~~

~~'''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.

== 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]] 2.5Å</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>

<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].

== 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]. Structure known Active Sites: FEA~~, ~~FEB~~, ~~FMA and FMB~~. ~~Full crystallographic information is available from [http~~:~~//ispc~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=1E5D OCA].~~

~~==Reference==~~

From MEDLINE®/PubMed®, 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~~]]

[[Category: ~~Single protein~~]]

== References ==

[[Category: Carrondo~~, M.A.~~]]

[[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 Nov 5 12:49:59 2007''~~

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@@ Line 1: / Line 1: @@
-[[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>
-E5D 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]. Structure known Active Sites: FEA, FEB, FMA and FMB. 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 Nov  5 12:49:59 2007''