1cc1
From Proteopedia
(New page: 200px<br /><applet load="1cc1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1cc1, resolution 2.15Å" /> '''CRYSTAL STRUCTURE OF...) |
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| - | [[Image:1cc1.gif|left|200px]]<br /><applet load="1cc1" size=" | + | [[Image:1cc1.gif|left|200px]]<br /><applet load="1cc1" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1cc1, resolution 2.15Å" /> | caption="1cc1, resolution 2.15Å" /> | ||
'''CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM'''<br /> | '''CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM'''<br /> | ||
==Overview== | ==Overview== | ||
| - | BACKGROUND: [NiFeSe] hydrogenases are metalloenzymes that catalyze the | + | BACKGROUND: [NiFeSe] hydrogenases are metalloenzymes that catalyze the reaction H2<-->2H+ + 2e-. They are generally heterodimeric, contain three iron-sulfur clusters in their small subunit and a nickel-iron-containing active site in their large subunit that includes a selenocysteine (SeCys) ligand. RESULTS: We report here the X-ray structure at 2.15 A resolution of the periplasmic [NiFeSe] hydrogenase from Desulfomicrobium baculatum in its reduced, active form. A comparison of active sites of the oxidized, as-prepared, Desulfovibrio gigas and the reduced D. baculatum hydrogenases shows that in the reduced enzyme the nickel-iron distance is 0.4 A shorter than in the oxidized enzyme. In addition, the putative oxo ligand, detected in the as-prepared D. gigas enzyme, is absent from the D. baculatum hydrogenase. We also observe higher-than-average temperature factors for both the active site nickel-selenocysteine ligand and the neighboring Glu18 residue, suggesting that both these moieties are involved in proton transfer between the active site and the molecular surface. Other differences between [NiFeSe] and [NiFe] hydrogenases are the presence of a third [4Fe4S] cluster replacing the [3Fe4S] cluster found in the D. gigas enzyme, and a putative iron center that substitutes the magnesium ion that has already been described at the C terminus of the large subunit of two [NiFe] hydrogenases. CONCLUSIONS: The heterolytic cleavage of molecular hydrogen seems to be mediated by the nickel center and the selenocysteine residue. Beside modifying the catalytic properties of the enzyme, the selenium ligand might protect the nickel atom from oxidation. We conclude that the putative oxo ligand is a signature of inactive 'unready' [NiFe] hydrogenases. |
==About this Structure== | ==About this Structure== | ||
| - | 1CC1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Desulfomicrobium_baculatum Desulfomicrobium baculatum] with NI, FE2, SF4, FCO and H2S as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http:// | + | 1CC1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Desulfomicrobium_baculatum Desulfomicrobium baculatum] with <scene name='pdbligand=NI:'>NI</scene>, <scene name='pdbligand=FE2:'>FE2</scene>, <scene name='pdbligand=SF4:'>SF4</scene>, <scene name='pdbligand=FCO:'>FCO</scene> and <scene name='pdbligand=H2S:'>H2S</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CC1 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Ferredoxin hydrogenase]] | [[Category: Ferredoxin hydrogenase]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Fontecilla-Camps, J | + | [[Category: Fontecilla-Camps, J C.]] |
[[Category: Frey, M.]] | [[Category: Frey, M.]] | ||
[[Category: Garcin, E.]] | [[Category: Garcin, E.]] | ||
| - | [[Category: Hatchikian, E | + | [[Category: Hatchikian, E C.]] |
[[Category: Vernede, X.]] | [[Category: Vernede, X.]] | ||
[[Category: Volbeda, A.]] | [[Category: Volbeda, A.]] | ||
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[[Category: oxidoreductase]] | [[Category: oxidoreductase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:04:32 2008'' |
Revision as of 10:04, 21 February 2008
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CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM
Overview
BACKGROUND: [NiFeSe] hydrogenases are metalloenzymes that catalyze the reaction H2<-->2H+ + 2e-. They are generally heterodimeric, contain three iron-sulfur clusters in their small subunit and a nickel-iron-containing active site in their large subunit that includes a selenocysteine (SeCys) ligand. RESULTS: We report here the X-ray structure at 2.15 A resolution of the periplasmic [NiFeSe] hydrogenase from Desulfomicrobium baculatum in its reduced, active form. A comparison of active sites of the oxidized, as-prepared, Desulfovibrio gigas and the reduced D. baculatum hydrogenases shows that in the reduced enzyme the nickel-iron distance is 0.4 A shorter than in the oxidized enzyme. In addition, the putative oxo ligand, detected in the as-prepared D. gigas enzyme, is absent from the D. baculatum hydrogenase. We also observe higher-than-average temperature factors for both the active site nickel-selenocysteine ligand and the neighboring Glu18 residue, suggesting that both these moieties are involved in proton transfer between the active site and the molecular surface. Other differences between [NiFeSe] and [NiFe] hydrogenases are the presence of a third [4Fe4S] cluster replacing the [3Fe4S] cluster found in the D. gigas enzyme, and a putative iron center that substitutes the magnesium ion that has already been described at the C terminus of the large subunit of two [NiFe] hydrogenases. CONCLUSIONS: The heterolytic cleavage of molecular hydrogen seems to be mediated by the nickel center and the selenocysteine residue. Beside modifying the catalytic properties of the enzyme, the selenium ligand might protect the nickel atom from oxidation. We conclude that the putative oxo ligand is a signature of inactive 'unready' [NiFe] hydrogenases.
About this Structure
1CC1 is a Protein complex structure of sequences from Desulfomicrobium baculatum with , , , and as ligands. Active as Ferredoxin hydrogenase, with EC number 1.12.7.2 Full crystallographic information is available from OCA.
Reference
The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center., Garcin E, Vernede X, Hatchikian EC, Volbeda A, Frey M, Fontecilla-Camps JC, Structure. 1999 May;7(5):557-66. PMID:10378275
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