The \u3cem\u3edapE\u3c/em\u3e-encoded \u3cem\u3eN\u3c/em\u3e-Succinyl-l,l-Diaminopimelic Acid Desuccinylase from \u3cem\u3eHaemophilus influenzae\u3c/em\u3e Is a Dinuclear Metallohydrolase

The Zn K-edge extended X-ray absorption fine structure (EXAFS) spectra, of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) from Haemophilus influenzae have been recorded in the presence of one or two equivalents of Zn(II) (i.e. [Zn_(DapE)] and [ZnZn(DapE)]). The Fourier transforms of the Zn EXAFS are dominated by a peak at ca. 2.0 Å, which can be fit for both [Zn_(DapE)] and [ZnZn(DapE)], assuming ca. 5 (N,O) scatterers at 1.96 and 1.98 Å, respectively. A second-shell feature at ca. 3.34 Å appears in the [ZnZn(DapE)] EXAFS spectrum but is significantly diminished in [Zn_(DapE)]. These data show that DapE contains a dinuclear Zn(II) active site. Since no X-ray crystallographic data are available for any DapE enzyme, these data provide the first glimpse at the active site of DapE enzymes. In addition, the EXAFS data for DapE incubated with two competitive inhibitors, 2-carboxyethylphosphonic acid and 5-mercaptopentanoic acid, are also presented

Structural elements of metal selectivity in metal sensor proteins

Staphylococcus aureus CzrA and Mycobacterium tuberculosis NmtR are homologous zinc/cobalt-responsive and nickel/cobalt-responsive transcriptional repressors in vivo, respectively, and members of the ArsR/SmtB superfamily of prokaryotic metal sensor proteins. We show here that Zn(II) is the most potent negative allosteric regulator of czr operator/promoter binding in vitro with the trend Zn(II)>Co(II)≫Ni(II), whereas the opposite holds for the binding of NmtR to the nmt operator/promoter, Ni(II)>Co(II)>Zn(II). Characterization of the metal coordination complexes of CzrA and NmtR by UV/visible and x-ray absorption spectroscopies reveals that metals that form four-coordinate tetrahedral complexes with CzrA [Zn(II) and Co(II)] are potent regulators of DNA binding, whereas metals that form five- or six-coordinate complexes with NmtR [Ni(II) and Co(II)] are the strongest allosteric regulators in this system. Strikingly, the Zn(II) coordination complexes of CzrA and NmtR cannot be distinguished from one another by x-ray absorption spectroscopy, with the best fit a His-3-carboxylate complex in both cases. Inspection of the primary structures of CzrA and NmtR, coupled with previous functional data, suggests that three conserved His and one Asp from the C-terminal α5 helix donate ligands to create a four-coordinate complex in both CzrA and NmtR, with NmtR uniquely capable of expanding its coordination number in the Ni(II) and Co(II) complexes by recruiting additional His ligands from a C-terminal extension of the α5 helix

Implementation of Revision 19 of the TRUPACT-II Safety Analysis Report at Rocky Flats Environmental Technology Site

The U.S. Nuclear Regulatory Commission on July 27, 2001 approved Revision 19 of the TRUPACT-II Safety Analysis Report (SAR) and the associated TRUPACT-II Authorized Methods for Payload Control (TRAMPAC). Key initiatives in Revision 19 included matrix depletion, unlimited mixing of shipping categories, a flammability assessment methodology, and an alternative methodology for the determination of flammable gas generation rates. All U.S. Department of Energy (DOE) sites shipping transuranic (TRU) waste to the Waste Isolation Pilot Plant (WIPP) were required to implement Revision 19 methodology into their characterization and waste transportation programs by May 20, 2002. An implementation process was demonstrated by the Rocky Flats Environmental Technology Site (RFETS) in Golden, Colorado. The three-part process used by RFETS included revision of the site-specific TRAMPAC, an evaluation of the contact-handled TRU waste inventory against the regulations in Revision 19, and design and development of software to facilitate future inventory analyses

Bottlenecks and roadblocks in high-throughput XAS for structural genomics

Structural and functional characterization of the entire protein complement (the proteome) of an organism can provide an infrastructure upon which questions about biological pathways and systems biology can be framed. The technology necessary to perform this proteome-level structural and functional characterization is under development in numerous structural genomics and functional genomics initiatives. Given the ubiquity of metal active sites in a proteome, it seems appropriate to ask whether comprehensive local structural characterization of metal sites within a proteome (metalloproteomics) is either a valid or obtainable goal. With a proteome-wide knowledge of the active-site structures of all metalloproteins, one could start to ask how metal insertion, cluster assembly and metalloprotein expression are affected by growth conditions or developmental status etc. High-throughput X-ray absorption spectroscopy (HTXAS) is being developed as a technology for investigating the metalloproteome. In creating a pipeline from genome to metalloproteome, several bottlenecks to high-throughput determination of metal-site structures must be overcome. For example, automation of arraying small samples for XAS examination must be invented, automation of rapid data collection of multiple low-volume low-concentration samples must be developed, automation of data reduction and analysis must be perfected. Discussed here are the promises and the pitfalls of HTXAS development, including the results of initial feasibility experiments. © 2005 International Union of Crystallography Printed in Great Britain - all rights reserved