5xpj

From Proteopedia

Crystal Structure of Periplasmic glucose binding protein ppGBP deletion mutant- Del-ppGBP

Structural highlights

5xpj is a 2 chain structure with sequence from Pseudomonas putida CSV86. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H7BRJ8_9PSED

Publication Abstract from PubMed

Substrate-binding proteins (SBPs) are periplasmic proteins consisting of two alpha/beta domains joined by a hinge region with specificity towards cognate ligands. Based on three-dimensional fold, sugar-specific SBPs have been classified into cluster B and cluster D-I. The analysis of sequences and structures of sugar-binding pocket of cluster D-I SBPs revealed the presence of extra residues on two loops (L1, L2) and a helix (H1) in few members of this family, that binds specifically to monosaccharides. Presence of conserved histidine in L2 and tryptophan in H1 can be considered as the identity marks for the cluster D-I monosaccharide-binding SBPs. A glucose binding protein (ppGBP) from Pseudomonas putida CSV86 was found to contain a structural fold similar to oligosaccharide-binding cluster D-I SBPs, but functionally binds to only glucose due to constriction of its binding pocket mainly by L2 (375-382). ppGBP with partial deletion of L2 (ppGBPDeltaL2) was created, crystallized and biochemical characterization was performed. Compared to wild type ppGBP, the ppGBPDeltaL2 structure showed widening of the glucose-binding pocket with approximately 80% lower glucose binding. Our results show that the substrate specificity of SBPs can be altered by modulating the size of the binding pocket. Based on this, we propose a sub classification of cluster D-I SBPs into (i) cluster D-I(a)-monosaccharide-binding SBPs and (ii) cluster D-I(b)-oligosaccharide-binding SBPs. This study also provides the direct structural and functional correlation indicating that divergence of proteins may occur through insertions or deletions of sequences in the already existing SBPs leading to evolution at the functional level.

Structural modulation of a periplasmic sugar-binding protein probes into its evolutionary ancestry.,Pandey S, Phale PS, Bhaumik P J Struct Biol. 2018 Sep 20. pii: S1047-8477(18)30256-9. doi:, 10.1016/j.jsb.2018.09.006. PMID:30244006^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Pandey S, Phale PS, Bhaumik P. Structural modulation of a periplasmic sugar-binding protein probes into its evolutionary ancestry. J Struct Biol. 2018 Sep 20. pii: S1047-8477(18)30256-9. doi:, 10.1016/j.jsb.2018.09.006. PMID:30244006 doi:http://dx.doi.org/10.1016/j.jsb.2018.09.006