1.7A crystal structure of protein PG110 from Staphylococcus aureus

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

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This is version 1.4 of the entry. See complete history


The membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus binds the dipeptide GlyMet via side chain interactions.

Williams, W.A.Zhang, R.G.Zhou, M.Joachimiak, G.Gornicki, P.Missiakas, D.Joachimiak, A.

(2004) Biochemistry 43: 16193-16202

  • DOI: https://doi.org/10.1021/bi048877o
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

    Committee on Microbiology, Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58 Street, Chicago, Illinois 60637, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical protein PG110295Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: SA0422
Find proteins for A0A0H3JTG5 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore A0A0H3JTG5 
Go to UniProtKB:  A0A0H3JTG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JTG5
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.496α = 90
b = 73.883β = 90
c = 92.246γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations