1hfe

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Current revision

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

Structural highlights

1hfe is a 4 chain structure with sequence from 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 crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PHFS_DESVH 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

BACKGROUND: Many microorganisms have the ability to either oxidize molecular hydrogen to generate reducing power or to produce hydrogen in order to remove low-potential electrons. These reactions are catalyzed by two unrelated enzymes: the Ni-Fe hydrogenases and the Fe-only hydrogenases. RESULTS: We report here the structure of the heterodimeric Fe-only hydrogenase from Desulfovibrio desulfuricans - the first for this class of enzymes. With the exception of a ferredoxin-like domain, the structure represents a novel protein fold. The so-called H cluster of the enzyme is composed of a typical [4Fe-4S] cubane bridged to a binuclear active site Fe center containing putative CO and CN ligands and one bridging 1, 3-propanedithiol molecule. The conformation of the subunits can be explained by the evolutionary changes that have transformed monomeric cytoplasmic enzymes into dimeric periplasmic enzymes. Plausible electron- and proton-transfer pathways and a putative channel for the access of hydrogen to the active site have been identified. CONCLUSIONS: The unrelated active sites of Ni-Fe and Fe-only hydrogenases have several common features: coordination of diatomic ligands to an Fe ion; a vacant coordination site on one of the metal ions representing a possible substrate-binding site; a thiolate-bridged binuclear center; and plausible proton- and electron-transfer pathways and substrate channels. The diatomic coordination to Fe ions makes them low spin and favors low redox states, which may be required for catalysis. Complex electron paramagnetic resonance signals typical of Fe-only hydrogenases arise from magnetic interactions between the [4Fe-4S] cluster and the active site binuclear center. The paucity of protein ligands to this center suggests that it was imported from the inorganic world as an already functional unit.

Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center.,Nicolet Y, Piras C, Legrand P, Hatchikian CE, Fontecilla-Camps JC Structure. 1999 Jan 15;7(1):13-23. PMID:10368269^[1]

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

References

↑ Nicolet Y, Piras C, Legrand P, Hatchikian CE, Fontecilla-Camps JC. Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center. Structure. 1999 Jan 15;7(1):13-23. PMID:10368269

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='1hfe' size='340' side='right'caption='[[1hfe]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1hfe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_subsp._vulgaris_str._hildenborough Desulfovibrio vulgaris subsp. vulgaris str. hildenborough]. 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 crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1HFE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1hfe]] is a 4 chain structure with sequence from [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 crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HFE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </span></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=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1hfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hfe OCA], [http://pdbe.org/1hfe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1hfe RCSB], [http://www.ebi.ac.uk/pdbsum/1hfe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1hfe 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=1hfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hfe OCA], [https://pdbe.org/1hfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hfe RCSB], [https://www.ebi.ac.uk/pdbsum/1hfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hfe ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PHFS_DESVH PHFS_DESVH]] 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. [[http://www.uniprot.org/uniprot/PHFL_DESVH PHFL_DESVH]] 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.
+[https://www.uniprot.org/uniprot/PHFS_DESVH PHFS_DESVH] 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 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 1hfe" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Teaching Scenes%2C Tutorials%2C and Educators' Pages|Teaching Scenes%2C Tutorials%2C and Educators' Pages]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Desulfovibrio vulgaris subsp. vulgaris str. hildenborough]]
+[[Category: Desulfovibrio vulgaris str. Hildenborough]]
-[[Category: Ferredoxin hydrogenase]]
 [[Category: Hydrogenase]]
 [[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Fontecilla-Camps, J C]]
+[[Category: Fontecilla-Camps JC]]
-[[Category: Hatchikian, E C]]
+[[Category: Hatchikian EC]]
-[[Category: Legrand, P]]
+[[Category: Legrand P]]
-[[Category: Nicolet, Y]]
+[[Category: Nicolet Y]]
-[[Category: Piras, C]]
+[[Category: Piras C]]
-[[Category: Fe-only hydrogenase]]
-[[Category: Hydrogene metabolism]]
-[[Category: Periplasm]]

1hfe

From Proteopedia

Current revision

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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