title: Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS).
abstract: 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(S2C2H4)(CO)2(PMe3)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. For Hmd, 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 approximately 311 cm(-1) and another reproducible feature at approximately 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 five-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A "truncated" model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site.
authors.affiliation: Department of Applied Science, University of California, Davis, California 95616, USA.
authors.forename: Yisong
authors.initials: Y
authors.lastname: Guo
authors.forename: Hongxin
authors.initials: H
authors.lastname: Wang
authors.forename: Yuming
authors.initials: Y
authors.lastname: Xiao
authors.forename: Sonja
authors.initials: S
authors.lastname: Vogt
authors.forename: Rudolf K
authors.initials: RK
authors.lastname: Thauer
authors.forename: Seigo
authors.initials: S
authors.lastname: Shima
authors.forename: Phillip I
authors.initials: PI
authors.lastname: Volkers
authors.forename: Thomas B
authors.initials: TB
authors.lastname: Rauchfuss
authors.forename: Vladimir
authors.initials: V
authors.lastname: Pelmenschikov
authors.forename: David A
authors.initials: DA
authors.lastname: Case
authors.forename: Ercan E
authors.initials: EE
authors.lastname: Alp
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Sturhahn
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Yoda
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Cramer
mesh_terms: D003198:Computer Simulation; D006864:Hydrogenase / Q000737:chemistry* / Q000378:metabolism*; D007501:Iron / Q000737:chemistry*; D007506:Iron-Sulfur Proteins / Q000737:chemistry* / Q000378:metabolism*; D017013:Methanobacteriaceae / Q000201:enzymology; D008958:Models, Molecular; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular; D013455:Sulfur / Q000737:chemistry*; D014732:Vibration
chemical_list: D007506:Iron-Sulfur Proteins; D013455:Sulfur; D007501:Iron; C118830:iron hydrogenase; D006864:Hydrogenase