title: NMR reveals structural rearrangements associated to substrate insertion in nucleotide-adding enzymes.
abstract: The protein NP_344798.1 from Streptococcus pneumoniae TIGR4 exhibits a head and base-interacting neck domain architecture, as observed in class II nucleotide-adding enzymes. Although it has less than 20% overall sequence identity with any member of this enzyme family, the residues involved in substrate-recognition and catalysis are highly conserved in NP_344798.1. NMR studies showed binding affinity of NP_344798.1 for nucleotides and revealed μs to ms time scale rate processes involving residues constituting the active site. The results thus obtained indicate that large-amplitude rearrangements of regular secondary structures facilitate the penetration of the substrate into the occluded nucleotide-binding site of NP_344798.1 and, by inference based on sequence and structural homology, probably a wide range of other nucleotide-adding enzymes.
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037.|Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, 92037.|Joint Center for Structural Genomics, The Scripps Research Insitute, La Jolla, California, 92037, http://www.jcsg.org.
authors.forename: Biswaranjan
authors.initials: B
authors.lastname: Mohanty
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037.|Joint Center for Structural Genomics, The Scripps Research Insitute, La Jolla, California, 92037, http://www.jcsg.org.
authors.forename: Michael
authors.initials: M
authors.lastname: Geralt
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037.|Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, 92037.|Joint Center for Structural Genomics, The Scripps Research Insitute, La Jolla, California, 92037, http://www.jcsg.org.
authors.forename: Kurt
authors.initials: K
authors.lastname: Wüthrich
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037.|Joint Center for Structural Genomics, The Scripps Research Insitute, La Jolla, California, 92037, http://www.jcsg.org.
authors.forename: Pedro
authors.initials: P
authors.lastname: Serrano
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D002384:Catalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D009711:Nucleotides / Q000378:metabolism*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D013296:Streptococcus pneumoniae / Q000737:chemistry / Q000201:enzymology*; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D009711:Nucleotides
keywords: DUF925; PF06042; nucleotide-binding protein; protein dynamics; protein structure; solution NMR