Artificial nucleotide-binding protein (ANBP) in a complex with bound ADP
A new technique called 'in vitro evolution' is able to produce proteins with novel folds and tailored functions. It is hoped that this technique which generates many proteins in vitro can contribute to solving important chemical, biochemical or therapeutic issues and to producing tailored highly specific molecules useful as medicines or biosensors.
Recently the first structure of a protein created by in vitro evolution has been determined by X-ray crystallographic analysis. Artificial nucleotide-binding protein (ANBP) is an ATP analog (ADP)-binding protein resulting from in vitro evolution using a random-sequence library. The crystal structure of ANBP expressed in Escherichia coli has been determined in a complex with bound ADP. This protein has a novel ADP and Zn ion binding fold, which consists of a three-stranded antiparallel beta-sheet and two nonadjacent alpha-helices. Protein folding in ANBP is stabilized by the hydrophobic core of the protein and by tetrahedral coordination of a Zn ion to the typical CXXCXnCXXC motif. In this structure, the adenine and ribose moieties of ADP interact with the aromatic residues of ANBP via stacking interactions in the same way as in naturally occurring ATP-binding proteins. Additionally, some polar residues of ANBP interact with the ADP phosphate group via hydrogen bonds. This may explain the higher binding affinity for ADP compared to other ligands such as GTP, CTP and AMP.
Protein Data Bank (PDB)
Lo Surdo, P. Walsh, M.A. Sollazzo, M.; "A Novel Adp- and Zinc-Binding Fold from Function-Directed in Vitro Evolution"; Nat.Struct.Mol.Biol.; (2004) 11:382-383. PubMed: 15024384
author: Yuko Tsuchiya