The Crystal Structure of the Apoenzyme of the Iron–Sulphur Cluster-free Hydrogenase

Pilak, Oliver; Mamat, B.; Vogt, Sonja; Hagemeier, Christoph H.; Thauer, Rudolf K.; Shima, Seigo; Vonrhein, Clemens; Warkentin, Eberhard; Ermler, Ulrich

doi:10.1016/j.jmb.2006.02.035

Cited by 107 publications

(111 citation statements)

References 43 publications

(45 reference statements)

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“…Of the three conserved cysteine residues (Cys10, Cys176 and Cys250), only Cys176 is essential for enzyme activity [12]. Cys176 is also considered an attractive ligand candidate because it is positioned at an appropriate distance from the mononucleotide-binding site at the bottom of an intersubunit cleft [13]. Additional evidence for single cysteine coordination comes from the recent EXAFS analysis, which found 1 Fe-S interaction at 2.31 Å, along with 2 Fe-C at 1.80 Å and 1 N or O atom at 2.03 Å [12].…”

Section: Introductionmentioning

confidence: 99%

Characterization of the Fe Site in Iron−Sulfur Cluster-Free Hydrogenase (Hmd) and of a Model Compound via Nuclear Resonance Vibrational Spectroscopy (NRVS)

et al. 2008

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We have used 57 Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur-cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO) 2 -ligated Fe model compound, Fe(S 2 C 2 H 4 )(CO) 2 (PMe 3 ) 2 , as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results.Previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm −1 , interpreted as evidence for cis-Fe(CO) 2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm −1 , consistent with the proposed cis-Fe(CO) 2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at ~311 cm −1 , and another reproducible feature at ~380 cm −1 . The 57 Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a 5-coordinate cis-(CO) 2 -ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a 3-dimensional structure for the active site.

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Section: Introductionmentioning

confidence: 99%

Characterization of the Fe Site in Iron−Sulfur Cluster-Free Hydrogenase (Hmd) and of a Model Compound via Nuclear Resonance Vibrational Spectroscopy (NRVS)

et al. 2008

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“…The third class of hydrogenases, the [Fe] hydrogenases, contain a single iron atom in their cofactors [12][13][14]. This type of enzyme is also called the iron-sulfur-cluster-free hydrogenase [15], or ''Hmd'' (H 2 -forming N 5 ,N 10 -methylenetetrahydromethanopterin dehydrogenase).…”

Section: Introductionmentioning

confidence: 99%

Spin distribution of the H-cluster in the Hox–CO state of the [FeFe] hydrogenase from Desulfovibrio desulfuricans: HYSCORE and ENDOR study of 14N and 13C nuclear interactions

et al. 2008

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“…They are grouped into three phylogenetically distinct classes as follows: the di-iron [FeFe], nickel-iron [NiFe], and iron-sulfur cluster-free [Fe] hydrogenases (2)(3)(4)(5)(6). The basic module of [NiFe] hydrogenases consists of two subunits, a large subunit that contains the [NiFe] active site and a small subunit that accommodates one to three electron-transferring iron-sulfur clusters (2,7,8).…”

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Spectroscopic Insights into the Oxygen-tolerant Membrane-associated [NiFe] Hydrogenase of Ralstonia eutropha H16

Saggu

Zebger

Ludwig

et al. 2009

Journal of Biological Chemistry

106

209

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Hydrogenases are metalloenzymes that catalyze the reversible cleavage of H 2 into protons and electrons and play a pivotal role in the energy metabolism of many microorganisms (1). They are grouped into three phylogenetically distinct classes as follows: the di-iron [FeFe], nickel-iron [NiFe], and iron-sulfur cluster-free [Fe] hydrogenases (2-6). The basic module of [NiFe] hydrogenases consists of two subunits, a large subunit that contains the [NiFe] active site and a small subunit that accommodates one to three electron-transferring iron-sulfur

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The Crystal Structure of the Apoenzyme of the Iron–Sulphur Cluster-free Hydrogenase

Cited by 107 publications

References 43 publications

Characterization of the Fe Site in Iron−Sulfur Cluster-Free Hydrogenase (Hmd) and of a Model Compound via Nuclear Resonance Vibrational Spectroscopy (NRVS)

Characterization of the Fe Site in Iron−Sulfur Cluster-Free Hydrogenase (Hmd) and of a Model Compound via Nuclear Resonance Vibrational Spectroscopy (NRVS)

Spin distribution of the H-cluster in the Hox–CO state of the [FeFe] hydrogenase from Desulfovibrio desulfuricans: HYSCORE and ENDOR study of 14N and 13C nuclear interactions

Spectroscopic Insights into the Oxygen-tolerant Membrane-associated [NiFe] Hydrogenase of Ralstonia eutropha H16

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