Structure of an intermediate of coenzyme B12 catalysis by EXAFS: Co2+ B12

Sagi, Irit; Wirt, Michael D.; Chen, Eefei; Frisbie, Suzanne M.; Chance, Mark R.

doi:10.1021/ja00180a001

Cited by 49 publications

(46 citation statements)

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“…Fitting these data to models can define the extent to which the zinc sites resemble one another. We measured the distances and Debye-Waller factors of these scatterers by Fourier filtering, back-transforming, and nonlinear least-squares fitting of the peptide and virus data to the models (19,(27)(28)(29). The observed truncation artifacts are minimized by matching the window functions of the model compounds and the unknowns.…”

Section: Resultsmentioning

confidence: 99%

“…The distance errors are estimated by a number of methods described previously (19,28). Variations in the individual Zn-S distances are not resolved by this procedure; data ofthis k range are unable to resolve contributions that are separated by -O.…”

Section: Resultsmentioning

confidence: 99%

“…Data analysis with fixed coordination numbers was carried out as described previously, using the University of Washington EXAFS package on a VAX computer (19). We compared several fits with different ratios of sulfur and nitrogen coordination numbers (S:N) held fixed in the fitting procedure (Tables 1 and 2).…”

Section: Resultsmentioning

confidence: 99%

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Extended x-ray absorption fine structure studies of a retrovirus: equine infectious anemia virus cysteine arrays are coordinated to zinc.

Chance

Sagi

Wirt

et al. 1992

Proc. Natl. Acad. Sci. U.S.A.

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Zinc finger arrays have been established as a critical structural feature of proteins involved in DNA recognition. Retroviral nudeocapsid proteins, which are involved in the binding of viral RNA, contain conserved cysteine-rich arrays that have been suggested to coordinate zinc. We provide metalloprotein structural data from an intact virus preparation that validate this hypothesis. Extended x-ray absorption fine structure (EXAFS) spectroscopy of well-characterized and active preparations of equine infectious anemia virus, compared with a peptide with known coordination and in combination with available biochemical and genetic data, defines a Cys3Hisj coordination environment for zinc. The average ofthe Zn-S distances is 2.30(1) A and that of the Zn-N distance (to histidine) is 2.01(3) A.Zinc finger domains are known to be of great importance in a number ofproteins that are involved in nucleic acid binding and transcriptional control. All known retroviral nucleocapsid (NC) proteins contain at least one sequence of the form Cys-Xaa2-Cys-Xaa4-His-Xaa4-Cys, where Xaa represents various amino acids (1-4). Site-directed mutagenesis experiments involving point mutations of cysteine, histidine, and adjacent residues in the NC protein of murine leukemia virus indicate that the conserved arrays are intimately involved in retroviral RNA recognition, since these mutants give rise to virus particles with little or no detectible viral RNA (5, 6). Subsequent genetic experiments with human immunodeficiency virus type 1 (HIV-1) gag domains, which have two cysteine arrays rather than one, reveal that mutations in either Cys-His array reduce RNA packaging considerably, and infectivity even more drastically (7,8).Prior investigations have conclusively shown that synthetic peptides based on these conserved retroviral sequences bind Zn2+ tightly and stoichiometrically (also Co2+ and Cd2+), and a wealth of spectroscopic evidence points to a three-cysteine one-histidine coordination for metals bound to these peptides (4,(9)(10)(11). The relevance of the peptides to virus function has been questioned, since the zinc content of avian myeloblastosis virus is reportedly insufficient to populate the cysteine arrays (12). However, more recent evidence clearly shows that the zinc content of HIV-1 and human T-cell leukemia virus type I (HTLV-I) is present in near stoichiometric amounts to the NC protein cysteine arrays (13). Thus, the potential importance of retroviral cysteine arrays and zinc to the physiological functions of nucleic acid binding and infectivity is illustrated by a wide range of investigations. We describe experiments that probe the zinc environment of concentrated preparations of equine infectious anemia virus (EIAV), a lentivirus (14, 15), using extended x-ray absorption fine structure (EXAFS) spectroscopy. Data obtained from analysis of virus was compared to that from a well-characterized 18-residue retroviral-type zinc finger peptide, based on sequences from HIV-1. This peptide has the sequence Val-Lys-Cys-Phe-As...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Extended x-ray absorption fine structure studies of a retrovirus: equine infectious anemia virus cysteine arrays are coordinated to zinc.

Chance

Sagi

Wirt

et al. 1992

Proc. Natl. Acad. Sci. U.S.A.

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“…The Ge detector was run at internal count rates of 40,000 counts channel-' s-l to minimize dead time losses. Data for EIAV and MMTV samples were collected at 170 K using a liquid nitrogen cryostat to limit sample damage and to minimize the thermal component of Debye-Waller factors (which leads to maximum differences in backscattering for chemically distinct ligands) (Sagi et al, 1990).…”

Section: Exafs Data Collection and Processingmentioning

confidence: 99%

Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution‐state structure of the nucleocapsid protein from HIV‐1

Henderson²,

et al. 1992

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All retroviral nucleocapsid (NC) proteins contain one or two copies of an invariant 3Cys‐1His array (CCHC = C‐X2‐C‐X4‐H‐X4‐C; C = Cys, H = His, X = variable amino acid) that are essential for RNA genome packaging and infectivity and have been proposed to function as zinc‐binding domains. Although the arrays are capable of binding zinc in vitro, the physiological relevance of zinc coordination has not been firmly established. We have obtained zinc‐edge extended X‐ray absorption fine structure (EXAFS) spectra for intact retroviruses in order to determine if virus‐bound zinc, which is present in quantities nearly stoichiometric with the CCHC arrays (Bess, J.W., Jr., Powell, P.J., Issaq, H.J., Schumack, L.J., Grimes, M.K., Henderson, L.E., & Arthur, L.O., 1992, J. Virol. 66, 840–847), exists in a unique coordination environment. The viral EXAFS spectra obtained are remarkably similar to the spectrum of a model CCHC zinc finger peptide with known 3Cys‐1His zinc coordination structure. This finding, combined with other biochemical results, indicates that the majority of the viral zinc is coordinated to the NC CCHC arrays in mature retroviruses. Based on these findings, we have extended our NMR studies of the HIV‐1 NC protein and have determined its three‐dimensional solution‐state structure. The CCHC arrays of HIV‐1 NC exist as independently folded, noninteracting domains on a flexible polypeptide chain, with conservatively substituted aromatic residues forming hydrophobic patches on the zinc finger surfaces. These residues are essential for RNA genome recognition, and fluorescence measurements indicate that at least one residue (Trp37) participates directly in binding to nucleic acids in vitro. The NC is only the third HIV‐1 protein to be structurally characterized, and the combined EXAFS, structural, and nucleic acid‐binding results provide a basis for the rational design of new NC‐targeted antiviral agents and vaccines for the control of AIDS.

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“…The Co K-edge E 0 of pristine B12 is 7724.5 eV, which value declines as the pyrolysis temperature increases. In previous studies, the Co oxidation state of pristine B12 was 3þ [25,26]. Scheuring et al used timeresolved X-ray absorption spectroscopy to study pristine B12-Co(III) and base-off B12-Co(II), and found that the E 0 of Co (II) was lower than that of Co(III) by approximately 4.0e6.0 eV [27].…”

Section: Structure Analysismentioning

confidence: 99%

Preparation of non-precious metal catalysts for PEMFC cathode from pyrolyzed vitamin B12

Chang

Hsu

Huang

et al. 2012

International Journal of Hydrogen Energy

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Structure of an intermediate of coenzyme B12 catalysis by EXAFS: Co2+ B12

Cited by 49 publications

References 1 publication

Extended x-ray absorption fine structure studies of a retrovirus: equine infectious anemia virus cysteine arrays are coordinated to zinc.

Extended x-ray absorption fine structure studies of a retrovirus: equine infectious anemia virus cysteine arrays are coordinated to zinc.

Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution‐state structure of the nucleocapsid protein from HIV‐1

Preparation of non-precious metal catalysts for PEMFC cathode from pyrolyzed vitamin B12

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