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NMR Solution Structure, Backbone Mobility, and Homology Modeling of c ‐Type Cytochromes from Gram‐Positive Bacteria
Author(s) -
Banci Lucia,
Bertini Ivano,
Ciurli Stefano,
Dikiy Alexander,
Dittmer Jens,
Rosato Antonio,
Sciara Giuliano,
Thompsett Andrew R.
Publication year - 2002
Publication title -
chembiochem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.05
H-Index - 126
eISSN - 1439-7633
pISSN - 1439-4227
DOI - 10.1002/1439-7633(20020402)3:4<299::aid-cbic299>3.0.co;2-0
Subject(s) - chemistry , crystallography , crystal structure , cytochrome c , protein structure , heme , cytochrome , dihedral angle , stereochemistry , molecule , biochemistry , hydrogen bond , organic chemistry , enzyme , mitochondrion
The solution structure of oxidized cytochrome c 553 (71 amino acid residues) from the Gram‐positive bacterium Bacillus pasteurii is here reported and compared with the available crystal structure. The solution structure is obtained from 1609 meaningful NOE data (22.7 per residue), 76 dihedral angles, and 59 pseudocontact shifts. The root mean square deviations from the average structure are 0.25±0.07 and 0.59±0.13 Å for the backbone and all heavy atoms, respectively, and the quality assessment of the structure is satisfactory. The solution structure closely reproduces the fold observed in the crystal structure. The backbone mobility was then investigated through amide 15 N relaxation rate and 15 N– 1 H NOE measurements. The protein is rigid in both the sub‐nanosecond and millisecond time scales, probably due to the relatively large heme:number of amino acids ratio. Modeling of eight c ‐type cytochromes from other Gram‐positive bacteria with a high sequence identity (>30 %) to the present cytochrome c 553 was performed. Analysis of consensus features accounts for the relatively low reduction potential as being due to extensive heme hydration and indicates residues 34–35, 44–46, 69–72, and 75 as a conserved hydrophobic patch for the interaction with a protein partner. At variance with mitochondrial c ‐type cytochrome, this protein does not experience pH‐dependent coordination equilibria. The reasons for this difference are analyzed.