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Comparative model of EutB from coenzyme B 12 ‐dependent ethanolamine ammonia‐lyase reveals a β 8 α 8 , TIM‐barrel fold and radical catalytic site structural features
Author(s) -
Sun Li,
Warncke Kurt
Publication year - 2006
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.20997
Subject(s) - lyase , protein data bank (rcsb pdb) , active site , chemistry , biochemistry , stereochemistry , dehydratase , protein structure , enzyme
The structure of the EutB protein from Salmonella typhimurium, which contains the active site of the coenzyme B 12 (adenosylcobalamin)‐dependent enzyme, ethanolamine ammonia‐lyase, has been predicted by using structural proteomics techniques of comparative modelling. The 453‐residue EutB protein displays no significant sequence identity with proteins of known structure. Therefore, secondary structure prediction and fold recognition algorithms were used to identify templates. Multiple three‐dimensional template matching (threading) servers identified predominantly β 8 α 8 , TIM‐barrel proteins, and in particular, the large subunits of diol dehydratase (PDB: 1eex:A, 1dio:A) and glycerol dehydratase (PDB: 1mmf:A), as templates. Consistent with this identification, the dehydratases are, like ethanolamine ammonia‐lyase, Class II coenzyme B 12 ‐dependent enzymes. Model building was performed by using MODELLER. Models were evaluated by using different programs, including PROCHECK and VERIFY3D. The results identify a β 8 α 8 , TIM‐barrel fold for EutB. The β 8 α 8 , TIM‐barrel fold is consistent with a central role of the α/β‐barrel structures in radical catalysis conducted by the coenzyme B 12 ‐ and S‐adenosylmethionine‐dependent (radical SAM) enzyme superfamilies. The EutB model and multiple sequence alignment among ethanolamine ammonia‐lyase, diol dehydratase, and glycerol dehydratase from different species reveal the following protein structural features: (1) a “cap” loop segment that closes the N‐terminal region of the barrel, (2) a common cobalamin cofactor binding topography at the C‐terminal region of the barrel, and (3) a β‐barrel‐internal guanidinium group from EutB R160 that overlaps the position of the active‐site potassium ion found in the dehydratases. R160 is proposed to have a role in substrate binding and radical catalysis. Proteins 2006. © 2006 Wiley‐Liss, Inc.