1e08

From Proteopedia

(Difference between revisions)

Current revision

Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking

Structural highlights

1e08 is a 3 chain structure with sequence from Desulfovibrio desulfuricans and Desulfovibrio vulgaris str. Hildenborough. The March 2009 RCSB PDB Molecule of the Month feature on Hydrogenase by David Goodsell is 10.2210/rcsb_pdb/mom_2009_3. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Hybrid , Solution NMR , Theoretical Model, 1 model
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PHFL_NITV2 May be involved in hydrogen uptake for the reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is likely to be the physiological electron carrier for the enzyme.

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

Fe-hydrogenase is a 54-kDa iron-sulfur enzyme essential for hydrogen cycling in sulfate-reducing bacteria. The x-ray structure of Desulfovibrio desulfuricans Fe-hydrogenase has recently been solved, but structural information on the recognition of its redox partners is essential to understand the structure-function relationships of the enzyme. In the present work, we have obtained a structural model of the complex of Fe-hydrogenase with its redox partner, the cytochrome c(553), combining docking calculations and NMR experiments. The putative models of the complex demonstrate that the small subunit of the hydrogenase has an important role in the complex formation with the redox partner; 50% of the interacting site on the hydrogenase involves the small subunit. The closest contact between the redox centers is observed between Cys-38, a ligand of the distal cluster of the hydrogenase and Cys-10, a ligand of the heme in the cytochrome. The electron pathway from the distal cluster of the Fe-hydrogenase to the heme of cytochrome c(553) was investigated using the software Greenpath and indicates that the observed cysteine/cysteine contact has an essential role. The spatial arrangement of the residues on the interface of the complex is very similar to that already described in the ferredoxin-cytochrome c(553) complex, which therefore, is a very good model for the interacting domain of the Fe-hydrogenase-cytochrome c(553).

Structural model of the Fe-hydrogenase/cytochrome c553 complex combining transverse relaxation-optimized spectroscopy experiments and soft docking calculations.,Morelli X, Czjzek M, Hatchikian CE, Bornet O, Fontecilla-Camps JC, Palma NP, Moura JJ, Guerlesquin F J Biol Chem. 2000 Jul 28;275(30):23204-10. PMID:10748163^[1]

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

References

↑ Morelli X, Czjzek M, Hatchikian CE, Bornet O, Fontecilla-Camps JC, Palma NP, Moura JJ, Guerlesquin F. Structural model of the Fe-hydrogenase/cytochrome c553 complex combining transverse relaxation-optimized spectroscopy experiments and soft docking calculations. J Biol Chem. 2000 Jul 28;275(30):23204-10. PMID:10748163 doi:10.1074/jbc.M909835199

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1e08"

@@ Line 1: / Line 1: @@
 ==Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking==
-<StructureSection load='1e08' size='340' side='right'caption='[[1e08]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='1e08' size='340' side='right'caption='[[1e08]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1e08]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans] and [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. The March 2009 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Hydrogenase''  by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_3 10.2210/rcsb_pdb/mom_2009_3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E08 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1E08 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1e08]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans] and [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._Hildenborough Desulfovibrio vulgaris str. Hildenborough]. The March 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Hydrogenase''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_3 10.2210/rcsb_pdb/mom_2009_3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E08 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PDT:1,3-PROPANEDITHIOL'>PDT</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Solution NMR , Theoretical Model, 1 model</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1hfe|1hfe]], [[1dvh|1dvh]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PDT:1,3-PROPANEDITHIOL'>PDT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1e08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e08 OCA], [http://pdbe.org/1e08 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e08 RCSB], [http://www.ebi.ac.uk/pdbsum/1e08 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e08 ProSAT]</span></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=1e08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e08 OCA], [https://pdbe.org/1e08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e08 RCSB], [https://www.ebi.ac.uk/pdbsum/1e08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e08 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PHFL_NITV2 PHFL_NITV2] May be involved in hydrogen uptake for the reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is likely to be the physiological electron carrier for the enzyme.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 13: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e0/1e08_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 30: / Line 32: @@
 ==See Also==
 *[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
-*[[Teaching Scenes%2C Tutorials%2C and Educators' Pages|Teaching Scenes%2C Tutorials%2C and Educators' Pages]]
 == References ==
 <references/>
@@ Line 36: / Line 37: @@
 </StructureSection>
 [[Category: Desulfovibrio desulfuricans]]
-[[Category: Desulfovibrio vulgaris]]
+[[Category: Desulfovibrio vulgaris str. Hildenborough]]
 [[Category: Hydrogenase]]
 [[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Bornet, O]]
+[[Category: Bornet O]]
-[[Category: Czjzek, M]]
+[[Category: Czjzek M]]
-[[Category: Fontecilla-Camps, J C]]
+[[Category: Fontecilla-Camps JC]]
-[[Category: Guerlesquin, F]]
+[[Category: Guerlesquin F]]
-[[Category: Hatchikian, C E]]
+[[Category: Hatchikian CE]]
-[[Category: Morelli, X]]
+[[Category: Morelli X]]
-[[Category: Moura, J J.G]]
+[[Category: Moura JJG]]
-[[Category: Palma, N P]]
+[[Category: Palma NP]]
-[[Category: Cytochrome c553]]
-[[Category: Electron transfer complex]]

1e08

From Proteopedia

Current revision

Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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