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Browsing gene banks for Fe 2 S 2 ferredoxins and structural modeling of 88 plant‐type sequences: An analysis of fold and function
Author(s) -
Bertini Ivano,
Luchinat Claudio,
Provenzani Alessandro,
Rosato Antonio,
Vasos Paul R.
Publication year - 2001
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10009
Subject(s) - ferredoxin , computational biology , structural motif , structural genomics , chemistry , crystallography , protein structure , biology , biochemistry , enzyme
Abstract One‐hundred‐and‐seventy‐nine sequences of Fe 2 S 2 ferredoxins and ferredoxin precursors were identified in and retrieved from currently available protein and cDNA databases. On the basis of their cluster‐binding patterns, these sequences were divided into three groups: those containing the CX 4 CX 2 CX n C pattern (plant‐type ferredoxins), those with the CX 5 CX 2 CX n C pattern (adrenodoxins), and those with a different pattern. These three groups contain, respectively, 139, 36, and 4 sequences. After excluding ferredoxin precursors in the first group, two subgroups were identified, again based on their cluster‐binding patterns: 88 sequences had the CX 4 CX 2 CX 29 C pattern, and 29 had the CX 4 CX 2 CX m C ( m ≠ 29) pattern. The structures of the 88 ferredoxins with the CX 4 CX 2 CX 29 C pattern were modeled based on the available experimental structures of nine proteins within this same group. The modeling procedure was tested by building structural models for the ferredoxins with known structures. The models resulted, on average, in being within 1 Å of the backbone root‐mean‐square deviation from the corresponding experimental structures. In addition, these structural models were shown to be of high quality by using assessment procedures based on energetic and stereochemical parameters. Thus, these models formed a reliable structural database for this group of ferredoxins, which is meaningful within the framework of current structural genomics efforts. From the analysis of the structural database generated it was observed that the secondary structural elements and the overall three‐dimensional structures are maintained throughout the superfamily. In particular, the residues in the hydrophobic core of the protein were found to be either absolutely conserved or conservatively substituted. In addition, certain solvent‐accessible charged groups, as well as hydrophobic groups, were found to be conserved to the same degree as the core residues. The patterns of conservation of exposed residues identified the regions of the protein that are critical for its function in electron transfer. An extensive analysis of protein—protein interactions is now possible. Some conserved interactions between residues have been identified and related to structural and/or functional features. All this information could not be obtained from the analyses of the primary sequences alone. Finally, the analysis of the sequences of the related subgroup featuring the CX 4 CX 2 CX m C ( m ≠ 29) cluster‐binding pattern in the light of the structural and functional insights provided by the inspection of the mentioned structural database affords some hints on the functional features of ferredoxins belonging to this subgroup. Proteins 2002;46:110–127. © 2001 Wiley‐Liss, Inc.