7C14

Crystal structure of a dinucleotide-binding protein (Q274A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form I)

Summary for 7C14

• Entry DOI: 10.2210/pdb7c14/pdb
• Descriptor: Sugar ABC transporter, periplasmic sugar-binding protein, GLYCEROL, [(1S,3R,3aR,6aS)-3-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-5,5-bis(oxidanyl)-1,3,3a,4,6,6a-hexahydrocyclopenta[c]furan-1-yl]methyl [(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate, ... (6 entities in total)
• Functional Keywords: c-di-gmp/amp, substrate-binding protein, thermus thermophilus, trna synthesis and/or modification, venus fly-trap mechanism, ugpb, transport protein
• Biological source: Thermus thermophilus HB8
• Total number of polymer chains: 2
• Total formula weight: 90506.79

Authors

Kanaujia, S.P.,Chandravanshi, M.,Samanta, R. (deposition date: 2020-05-02, release date: 2021-03-10, Last modification date: 2023-11-29)

Primary citation

Chandravanshi, M.,Samanta, R.,Kanaujia, S.P.
Structural and thermodynamic insights into the novel dinucleotide-binding protein of ABC transporter unveils its moonlighting function.
Febs J., 288:4614-4636, 2021

PubMed Abstract: Substrate (or solute)-binding proteins (SBPs) selectively bind the target ligands and deliver them to the ATP-binding cassette (ABC) transport system for their translocation. Irrespective of the different types of ligands, SBPs are structurally conserved. A wealth of structural details of SBPs bound to different types of ligands and the physiological basis of their import are available; however, the uptake mechanism of nucleotides is still deficient. In this study, we elucidated the structural details of an SBP endogenously bound to a novel ligand, a derivative of uridylyl-3'-5'-phospho-guanosine (U3G); thus, we named it a U3G-binding protein (U3GBP). To the best of our knowledge, this is the first report of U3G (and a dinucleotide) binding to the SBP of ABC transport system, and thus, U3GBP is classified as a first member of subcluster D-I SBPs. Thermodynamic data also suggest that U3GBP can bind phospholipid precursor sn-glycerophosphocholine (GPC) at a site other than the active site. Moreover, a combination of mutagenic and structural information reveals that the protein U3GBP follows the well-known 'Venus Fly-trap' mechanism for dinucleotide binding. DATABASES: Structural data are available in RCSB Protein Data Bank under the accession number(s) 7C0F, 7C0K, 7C0L, 7C0O, 7C0R, 7C0S, 7C0T, 7C0U, 7C0V, 7C0W, 7C0X, 7C0Y, 7C0Z, 7C14, 7C15, 7C16, 7C19, and 7C1B.

PubMed: 33599038
DOI: 10.1111/febs.15774

Experimental method

X-RAY DIFFRACTION (2.4 Å)