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 ls 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 nucleotideadding enzymes.

NMR in structural genomics to increase structural coverage of the protein universe

“…3), which shared less than 15% sequence identity with structural counterparts in the PDB, illustrate this situation. Structure determination of these three proteins revealed close three-dimensional structure similarity with functionally annotated proteins in the PDB [39][40][41][42]. In these scenarios, without obtaining additional information on the individual proteins, we were able to provide functional annotations for the newly studied proteins and their respective Pfam families [39][40][41][42].…”

“…3. Some of these proteins have previously been discussed in different contexts, where additional details of the structure determinations were given [39][40][41][42].…”

NMR in structural genomics to increase structural coverage of the protein universe

“…3. Some of these proteins have previously been discussed in different contexts, where additional details of the structure determinations were given [39][40][41][42].…”

“…3), which shared less than 15% sequence identity with structural counterparts in the PDB, illustrate this situation. Structure determination of these three proteins revealed close three-dimensional structure similarity with functionally annotated proteins in the PDB [39][40][41][42]. In these scenarios, without obtaining additional information on the individual proteins, we were able to provide functional annotations for the newly studied proteins and their respective Pfam families [39][40][41][42].…”