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A model‐based proposal for the role of UreF as a GTPase‐activating protein in the urease active site biosynthesis
Author(s) -
SalomoneStagni Marco,
Zambelli Barbara,
Musiani Francesco,
Ciurli Stefano
Publication year - 2007
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.21472
Subject(s) - active site , homology modeling , modeller , biochemistry , gtpase , chemistry , chaperone (clinical) , computational biology , molecular model , biology , enzyme , medicine , pathology
Abstract UreF is a protein that plays a role in the in vivo urease activation as a chaperone involved in the insertion of two Ni 2+ ions in the apo‐urease active site. The molecular details of this process are unknown. In the absence of any molecular information on the UreF protein class, and as a step toward the comprehension of the relationships between UreF function and structure, we applied a structural modeling approach to infer useful biochemical knowledge on Bacillus pasteurii UreF ( Bp UreF). Similarity searches and multiple alignment of UreF protein sequences indicated that this class of proteins has a low homology with proteins of known structure. Fold recognition methods were therefore used to identify useful protein structural templates to model the structure of Bp UreF. In particular, the templates belong to the class of GTPase‐activating proteins. Modeling of Bp UreF based on these templates was performed using the program MODELLER. The structure validation yielded good statistics, indicating that the model is plausible. This result suggests a role for UreF in urease active site biosynthesis as a regulator of the activity of UreG, a small G protein involved in the in vivo apo‐urease activation process and established to catalyze GTP hydrolysis. Proteins 2007. © 2007 Wiley‐Liss, Inc.