1hfe: Difference between revisions

Revision as of 18:47, 2 May 2008

Ligands:

, , , , , ,

Activity:

Ferredoxin hydrogenase, with EC number 1.12.7.2

Structural annotation:
Resources:	CATH : 1Hfel01, 1Hfel03, 1Hfel02, 1Hfem01, 1Hfem03, 1Hfem02, 1Hfes00, 1Hfet00 InterPro : Ipr017900, Ipr004108, Ipr017896, Ipr013352, Ipr009016, Ipr006311, Ipr008953, Ipr003149, Ipr017909 Pfam : PF00037, PF02906, PF02256 SCOP : d1hfel1, d1hfel2, d1hfem2, d1hfem1, d1hfes_, d1hfet_ UniProt : P07598, P07603

Evolutionary conservation:

Toggle Conservation Colors:

Rows = identical sequences:

Further Information:

Caveats,

Explanation,
Complete Results at ConSurfDB

Resources:

FirstGlance, OCA, RCSB, PDBsum

Coordinates:

save as pdb, mmCIF, xml

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

OverviewOverview

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.

About this StructureAbout this Structure

1HFE is a Protein complex structure of sequences from Desulfovibrio vulgaris. Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Fri May 2 18:47:40 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:1hfe.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1hfe |SIZE=350|CAPTION= <scene name='initialview01'>1hfe</scene>, resolution 1.600&Aring;
+The line below this paragraph, containing "STRUCTURE_1hfe", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <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>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <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>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1hfe|  PDB=1hfe  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<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://www.ebi.ac.uk/pdbsum/1hfe PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1hfe RCSB]</span>
-}}
 '''1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS'''
@@ Line 31: / Line 28: @@
 [[Category: Nicolet, Y.]]
 [[Category: Piras, C.]]
-[[Category: fe-only hydrogenase]]
+[[Category: Fe-only hydrogenase]]
-[[Category: hydrogene metabolism]]
+[[Category: Hydrogene metabolism]]
-[[Category: periplasm]]
+[[Category: Periplasm]]
-[[Category: x-ray crystallography]]
+[[Category: X-ray crystallography]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 18:47:40 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:04:02 2008''