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Nucleic Acids Research 2004 32(13):4015-4025; doi:10.1093/nar/gkh728
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Published online 2 August 2004

Nucleic Acids Research, Vol. 32 No. 13 © Oxford University Press 2004; all rights reserved

AdoMet radical proteins—from structure to evolution—alignment of divergent protein sequences reveals strong secondary structure element conservation

Yvain Nicolet and Catherine L. Drennan*

Department of Chemistry 16-573, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA

* To whom correspondence should be addressed. Tel: +1 617 253 5622; Fax: +1 617 258 7847; Email: cdrennan{at}mit.edu
Present address: Yvain Nicolet, Macromolecular Crystallography, European Synchrotron Radiation Facility, BP220, F-38043 Grenoble cedex, France

Received as resubmission May 19, 2004; Revised June 18, 2004; Accepted July 9, 2004

Eighteen subclasses of S-adenosyl-L-methionine (AdoMet) radical proteins have been aligned in the first bioinformatics study of the AdoMet radical superfamily to utilize crystallographic information. The recently resolved X-ray structure of biotin synthase (BioB) was used to guide the multiple sequence alignment, and the recently resolved X-ray structure of coproporphyrinogen III oxidase (HemN) was used as the control. Despite the low 9% sequence identity between BioB and HemN, the multiple sequence alignment correctly predicted all but one of the core helices in HemN, and correctly predicted the residues in the enzyme active site. This alignment further suggests that the AdoMet radical proteins may have evolved from half-barrel structures ({alpha}ß)4 to three-quarter-barrel structures ({alpha}ß)6 to full-barrel structures ({alpha}ß)8. It predicts that anaerobic ribonucleotide reductase (RNR) activase, an ancient enzyme that, it has been suggested, serves as a link between the RNA and DNA worlds, will have a half-barrel structure, whereas the three-quarter barrel, exemplified by HemN, will be the most common architecture for AdoMet radical enzymes, and fewer members of the superfamily will join BioB in using a complete ({alpha}ß)8 TIM-barrel fold to perform radical chemistry. These differences in barrel architecture also explain how AdoMet radical enzymes can act on substrates that range in size from 10 atoms to 608 residue proteins.


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