8UPI

Structure of a periplasmic peptide binding protein from Mesorhizobium sp. AP09 bound to aminoserine

8UPI の概要

• エントリーDOI: 10.2210/pdb8upi/pdb
• 分子名称: Peptide ABC transporter substrate-binding protein, CALCIUM ION, 1,2-ETHANEDIOL, ... (5 entities in total)
• 機能のキーワード: abc-transporter-associated periplasmic binding protein, peptide binding protein, amino acid binding protein, metal binding protein
• 由来する生物種: Mesorhizobium sp. AP09
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 57555.83

構造登録者

Frkic, R.L.,Smith, O.B.,Rahman, M.,Kaczmarski, J.A.,Jackson, C.J. (登録日: 2023-10-22, 公開日: 2023-11-08, 最終更新日: 2024-10-23)

主引用文献

Smith, O.B.,Frkic, R.L.,Rahman, M.G.,Jackson, C.J.,Kaczmarski, J.A.
Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides.
Biochemistry, 63:1322-1334, 2024

PubMed Abstract: Periplasmic solute-binding proteins (SBPs) are key ligand recognition components of bacterial ATP-binding cassette (ABC) transporters that allow bacteria to import nutrients and metabolic precursors from the environment. Periplasmic SBPs comprise a large and diverse family of proteins, of which only a small number have been empirically characterized. In this work, we identify a set of 610 unique uncharacterized proteins within the SBP_bac_5 family that are found in conserved operons comprising genes encoding (i) ABC transport systems and (ii) putative amidases from the FmdA_AmdA family. From these uncharacterized SBP_bac_5 proteins, we characterize a representative periplasmic SBP from sp. A09 (Ami_SBP) and show that Ami_SBP binds l-amino acid amides but not the corresponding l-amino acids. An X-ray crystal structure of Ami_SBP bound to l-serinamide highlights the residues that impart distinct specificity for l-amino acid amides and reveals a structural Ca binding site within one of the lobes of the protein. We show that the residues involved in ligand and Ca binding are conserved among the 610 SBPs from experimentally uncharacterized FmdA_AmdA amidase-associated ABC transporter systems, suggesting these homologous systems are also likely to be involved in the sensing, uptake, and metabolism of l-amino acid amides across many Gram-negative nitrogen-fixing soil bacteria. We propose that Ami_SBP is involved in the uptake of such solutes to supplement pathways such as the citric acid cycle and the glutamine synthetase-glutamate synthase pathway. This work expands our currently limited understanding of microbial interactions with l-amino acid amides and bacterial nitrogen utilization.

PubMed: 38696389
DOI: 10.1021/acs.biochem.4c00096

実験手法

X-RAY DIFFRACTION (1.55 Å)