Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS).
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.
Guo
Yisong
Y
Department of Applied Science, University of California, Davis, California 95616, USA.
Wang
Hongxin
H
Xiao
Yuming
Y
Vogt
Sonja
S
Thauer
Rudolf K
RK
Shima
Seigo
S
Volkers
Phillip I
PI
Rauchfuss
Thomas B
TB
Pelmenschikov
Vladimir
V
Case
David A
DA
Alp
Ercan E
EE
Sturhahn
Wolfgang
W
Yoda
Yoshitaka
Y
Cramer
Stephen P
SP
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
D007506:Iron-Sulfur Proteins; D013455:Sulfur; D007501:Iron; C118830:iron hydrogenase; D006864:Hydrogenase