Extended X-ray absorption fine structure and nuclear resonance vibrational spectroscopy reveal that NifB-co, a FeMo-co precursor, comprises a 6Fe core with an interstitial light atom.
NifB-co, an Fe-S cluster produced by the enzyme NifB, is an intermediate on the biosynthetic pathway to the iron molybdenum cofactor (FeMo-co) of nitrogenase. We have used Fe K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy together with (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to probe the structure of NifB-co while bound to the NifX protein from Azotobacter vinelandii. The spectra have been interpreted in part by comparison with data for the completed FeMo-co attached to the NafY carrier protein: the NafY:FeMo-co complex. EXAFS analysis of the NifX:NifB-co complex yields an average Fe-S distance of 2.26 A and average Fe-Fe distances of 2.66 and 3.74 A. Search profile analyses reveal the presence of a single Fe-X (X = C, N, or O) interaction at 2.04 A, compared to a 2.00 A Fe-X interaction found in the NafY:FeMo-co EXAFS. This suggests that the interstitial light atom (X) proposed to be present in FeMo-co has already inserted at the NifB-co stage of biosynthesis. The NRVS exhibits strong bands from Fe-S stretching modes peaking around 270, 315, 385, and 408 cm(-1). Additional intensity at approximately 185-200 cm(-1) is interpreted as a set of cluster "breathing" modes similar to those seen for the FeMo-cofactor. The strength and location of these modes also suggest that the FeMo-co interstitial light atom seen in the crystal structure is already in place in NifB-co. Both the EXAFS and NRVS data for NifX:NifB-co are best simulated using a Fe 6S 9X trigonal prism structure analogous to the 6Fe core of FeMo-co, although a 7Fe structure made by capping one trigonal 3S terminus with Fe cannot be ruled out. The results are consistent with the conclusion that the interstitial light atom is already present at an early stage in FeMo-co biosynthesis prior to the incorporation of Mo and R-homocitrate.
George
Simon J
SJ
Advanced Biological and Environmental X-ray Facility, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
Igarashi
Robert Y
RY
Xiao
Yuming
Y
Hernandez
Jose A
JA
Demuez
Marie
M
Zhao
Dehua
D
Yoda
Yoshitaka
Y
Ludden
Paul W
PW
Rubio
Luis M
LM
Cramer
Stephen P
SP
D000042:Absorption; D002244:Carbon / Q000737:chemistry; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods; D058085:Iron Compounds / Q000737:chemistry* / Q000378:metabolism; D015394:Molecular Structure; D008983:Molybdoferredoxin / Q000737:chemistry* / Q000378:metabolism; D009584:Nitrogen / Q000737:chemistry; D010100:Oxygen / Q000737:chemistry; D014965:X-Rays
D058085:Iron Compounds; D008983:Molybdoferredoxin; C085381:NifB cofactor; D002244:Carbon; D009584:Nitrogen; D010100:Oxygen