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Protein Sci. 2016 Apr;25(4):917-25. doi: 10.1002/pro.2872. Epub 2016 Jan 20.

NMR reveals structural rearrangements associated to substrate insertion in nucleotide-adding enzymes.

Author information

1
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037.
2
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, 92037.
3
Joint Center for Structural Genomics, The Scripps Research Insitute, La Jolla, California, 92037, http://www.jcsg.org.

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.

KEYWORDS:

DUF925; PF06042; nucleotide-binding protein; protein dynamics; protein structure; solution NMR

PMID:
26749007
PMCID:
PMC4941227
DOI:
10.1002/pro.2872
[Indexed for MEDLINE]
Free PMC Article

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