1P99

1.7A crystal structure of protein PG110 from Staphylococcus aureus

Summary for 1P99

• Entry DOI: 10.2210/pdb1p99/pdb
• Descriptor: Hypothetical protein PG110, GLYCINE, METHIONINE, ... (4 entities in total)
• Functional Keywords: structural genomics, psi, protein structure initiative, midwest center for structural genomics, mcsg, unknown function
• Biological source: Staphylococcus aureus subsp. aureus Mu50
• Total number of polymer chains: 1
• Total formula weight: 32737.18

Authors

Zhang, R.,Zhou, M.,Joachimiak, G.,Schneewind, O.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2003-05-09, release date: 2004-01-20, Last modification date: 2024-02-14)

Primary citation

Williams, W.A.,Zhang, R.G.,Zhou, M.,Joachimiak, G.,Gornicki, P.,Missiakas, D.,Joachimiak, A.
The membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus binds the dipeptide GlyMet via side chain interactions.
Biochemistry, 43:16193-16202, 2004

PubMed Abstract: Bacterial dipeptide ABC transporters function to import a wide range of dipeptide substrates. This ability to transport a wide variety of dipeptides is conferred by the cognate substrate binding protein (SBP) of these transporters. SBPs bind dipeptides with little regard for their amino acid content. Here, we report the 1.7 A resolution structure of lipoprotein-9 (SA0422) of Staphylococcus aureus in complex with the dipeptide glycylmethionine. Experimental characterization of the subcellular location of the protein confirmed that SA0422 is an acylated, peripheral membrane protein. This is the first structure determined for an SBP of a Gram-positive dipeptide ABC transporter. Usually, binding of dipeptides occurs in a binding pocket that is largely hydrated and able to accommodate the side chains of several different amino acid residues. Unlike any other known SBP, lipoprotein-9 binds the side chains of the glycylmethionine dipeptide through very specific interactions. Lipoprotein-9 shares significant structural and sequence homology with the MetQ family of methionine SBP. Sequence comparisons between MetQ-like proteins and lipoprotein-9 suggest that the residues forming the tight interactions with the methionine side chains of the ligand are highly conserved between lipoprotein-9 and MetQ homologues, while the residues involved in coordinating the glycine residue are not. Modeling of the Vibrio cholerae MetQ and lipoprotein-9 binding pockets can account for lipoprotein-9 substrate specificity toward glycylmethionine. For this reason, we have designated lipoprotein-9 GmpC, for glycylmethionine binding protein.

PubMed: 15610013
DOI: 10.1021/bi048877o

Experimental method

X-RAY DIFFRACTION (1.7 Å)