Biomaterial Database

Terminal Hydride Species in [FeFe]-Hydrogenases Are Vibrationally Coupled to the Active Site Environment. 2018

Cindy C Pham, and David W Mulder, and Vladimir Pelmenschikov, and Paul W King, and Michael W Ratzloff, and Hongxin Wang, and Nakul Mishra, and Esen E Alp, and Jiyong Zhao, and Michael Y Hu, and Kenji Tamasaku, and Yoshitaka Yoda, and Stephen P Cramer

Department of Chemistry, UC Davis, One Shields Ave, Davis, CA, 95616, USA.

A combination of nuclear resonance vibrational spectroscopy (NRVS), FTIR spectroscopy, and DFT calculations was used to observe and characterize Fe-H/D bending modes in CrHydA1 [FeFe]-hydrogenase Cys-to-Ser variant C169S. Mutagenesis of cysteine to serine at position 169 changes the functional group adjacent to the H-cluster from a -SH to -OH, thus altering the proton transfer pathway. The catalytic activity of C169S is significantly reduced compared to that of native CrHydA1, presumably owing to less efficient proton transfer to the H-cluster. This mutation enabled effective capture of a hydride/deuteride intermediate and facilitated direct detection of the Fe-H/D normal modes. We observed a significant shift to higher frequency in an Fe-H bending mode of the C169S variant, as compared to previous findings with reconstituted native and oxadithiolate (ODT)-substituted CrHydA1. On the basis of DFT calculations, we propose that this shift is caused by the stronger interaction of the -OH group of C169S with the bridgehead -NH- moiety of the active site, as compared to that of the -SH group of C169 in the native enzyme.

UI	MeSH Term	Description	Entries
D007501	Iron	A metallic element with atomic symbol Fe, atomic number 26, and atomic weight 55.85. It is an essential constituent of HEMOGLOBINS; CYTOCHROMES; and IRON-BINDING PROTEINS. It plays a role in cellular redox reactions and in the transport of OXYGEN.	Iron-56,Iron 56
D011522	Protons	Stable elementary particles having the smallest known positive charge, found in the nuclei of all elements. The proton mass is less than that of a neutron. A proton is the nucleus of the light hydrogen atom, i.e., the hydrogen ion.	Hydrogen Ions,Hydrogen Ion,Ion, Hydrogen,Ions, Hydrogen,Proton
D003013	Clostridium	A genus of motile or nonmotile gram-positive bacteria of the family Clostridiaceae. Many species have been identified with some being pathogenic. They occur in water, soil, and in the intestinal tract of humans and lower animals.
D006864	Hydrogenase	An enzyme found in bacteria. It catalyzes the reduction of FERREDOXIN and other substances in the presence of molecular hydrogen and is involved in the electron transport of bacterial photosynthesis.	Ferredoxin Hydrogenase,H2-Oxidizing Hydrogenase,Hydrogenlyase,H2 Oxidizing Hydrogenase,Hydrogenase, Ferredoxin,Hydrogenase, H2-Oxidizing
D000077318	Density Functional Theory	A theory that is used to describe the electronic ground state properties of matter. It forms the basis of methods in obtaining a solution to the Schrodinger equation for a many-body system, and to investigate the structural, magnetic, and electronic properties of molecules and materials.	Density Functional Calculations,Density Functional Computations,Density Functional Theory Calculations,Density Functional Theory Computations,Td-DFT,Td-DFT Calculations,Td-DFT Computations,Time-Dependent Density Functional Theory,Time-Dependent Density Functional Theory Calculations,Time-Dependent Density Functional Theory Computations,DFT Calculations,KS-DFT,Kohn-Sham Density Functional Theory,Calculation, Density Functional,Calculation, Td-DFT,Computation, Density Functional,Computation, Td-DFT,DFT Calculation,Density Functional Calculation,Density Functional Computation,Density Functional Theories,Functional Calculation, Density,Functional Calculations, Density,Functional Computation, Density,Kohn Sham Density Functional Theory,Td DFT Calculations,Td DFT Computations,Td-DFT Calculation,Td-DFT Computation,Time Dependent Density Functional Theory,Time Dependent Density Functional Theory Calculations,Time Dependent Density Functional Theory Computations
D016297	Mutagenesis, Site-Directed	Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.	Mutagenesis, Oligonucleotide-Directed,Mutagenesis, Site-Specific,Oligonucleotide-Directed Mutagenesis,Site-Directed Mutagenesis,Site-Specific Mutagenesis,Mutageneses, Oligonucleotide-Directed,Mutageneses, Site-Directed,Mutageneses, Site-Specific,Mutagenesis, Oligonucleotide Directed,Mutagenesis, Site Directed,Mutagenesis, Site Specific,Oligonucleotide Directed Mutagenesis,Oligonucleotide-Directed Mutageneses,Site Directed Mutagenesis,Site Specific Mutagenesis,Site-Directed Mutageneses,Site-Specific Mutageneses
D017550	Spectroscopy, Fourier Transform Infrared	A spectroscopic technique in which a range of wavelengths is presented simultaneously with an interferometer and the spectrum is mathematically derived from the pattern thus obtained.	FTIR,Fourier Transform Infrared Spectroscopy,Spectroscopy, Infrared, Fourier Transform
D045285	Desulfovibrio desulfuricans	The type species of gram-negative, anaerobic bacteria of the genus DESULFOVIBRIO. It is found in FRESHWATER; SOIL, and in marine or brackish water.
D020134	Catalytic Domain	The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.	Active Site,Catalytic Core,Catalytic Region,Catalytic Site,Catalytic Subunit,Reactive Site,Active Sites,Catalytic Cores,Catalytic Domains,Catalytic Regions,Catalytic Sites,Catalytic Subunits,Core, Catalytic,Cores, Catalytic,Domain, Catalytic,Domains, Catalytic,Reactive Sites,Region, Catalytic,Regions, Catalytic,Site, Active,Site, Catalytic,Site, Reactive,Sites, Active,Sites, Catalytic,Sites, Reactive,Subunit, Catalytic,Subunits, Catalytic