X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus

Day, M. W., Hsu, B. T., Joshua-Tor, L., Park, J. B., Zhou, Z. H., Adams, M. W. W., Rees, D. C. (1992) X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus. Protein Science, 1 (11). pp. 1494-1507. ISSN 09618368 (ISSN)

URL: https://www.ncbi.nlm.nih.gov/pubmed/1303768
DOI: 10.1002/pro.5560011111

Abstract

The structures of the oxidized and reduced forms of the rubredoxin from the archaebacterium, Pyrococcus furiosus, an organism that grows optimally at 100°C, have been determined by X-ray crystallography to a resolution of 1.8 Å. Crystals of this rubredoxin grow in space group P212121 with room temperature cell dimensions a = 34.6 Å, b = 35.5 Å, and c = 44.4 Å. Initial phases were determined by the method of molecular replacement using the oxidized form of the rubredoxin from the mesophilic eubacterium, Clostridium pasteurianum, as a starting model. The oxidized and reduced models of P. furiosus rubredoxin each contain 414 nonhydrogen protein atoms comprising 53 residues. The model of the oxidized form contains 61 solvent H2O oxygen atoms and has been refined with X-PLOR and TNT to a final R = 0.178 with root mean square (rms) deviations from ideality in bond distances and bond angles of 0.014 Å and 2.06°, respectively. The model of the reduced form contains 37 solvent H2O oxygen atoms and has been refined to R = 0.193 with rms deviations from ideality in bond lengths of 0.012 Å and in bond angles of 1.95°. The overall structure of P. furiosus rubredoxin is similar to the structures of mesophilic rubredoxins, with the exception of a more extensive hydrogen-bonding network in the β-sheet region and multiple electrostatic interactions (salt bridge, hydrogen bonds) of the Glu 14 side chain with groups on three other residues (the amino-terminal nitrogen of Ala 1; the indole nitrogen of Trp 3; and the amide nitrogen group of Phe 29). The influence of these and other features upon the thermostability of the P. furiosus protein is discussed.

Item Type: Paper
Uncontrolled Keywords: bacterial protein rubredoxin archaebacterium article nonhuman oxidation protein stability protein structure reduction thermostability X ray crystallography Amino Acid Sequence Archaea Comparative Study Crystallization Drug Stability Heat Hydrogen Bonding Mathematics Models, Molecular Molecular Sequence Data Oxidation-Reduction Protein Conformation Protein Structure, Secondary Rubredoxins Sequence Homology, Amino Acid Thermodynamics X-Ray Diffraction
Subjects: Investigative techniques and equipment > X-Ray Diffraction
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein structure rendering
Investigative techniques and equipment > x ray crystallography
CSHL Authors:
Communities: CSHL labs > Joshua-Tor lab
Depositing User: CSHL Librarian
Date Deposited: 20 Mar 2012 19:11
Last Modified: 06 Sep 2017 15:52
PMCID: PMC2142115
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Dataset ID:
URI: http://repository.cshl.edu/id/eprint/25506

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