Crystal structure of Lactococcus lactis GlnP substrate binding domain 2 (SBD2) in complex with glutamine at 0.95 A resolution

Experimental Data Snapshot

  • Resolution: 0.95 Å
  • R-Value Free: 0.120 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.115 

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Functional Diversity of Tandem Substrate-Binding Domains in ABC Transporters from Pathogenic Bacteria.

Fulyani, F.Schuurman-Wolters, G.K.Zagar, A.V.Guskov, A.Slotboom, D.J.Poolman, B.

(2013) Structure 21: 1879-1888

  • DOI: https://doi.org/10.1016/j.str.2013.07.020
  • Primary Citation of Related Structures:  
    4G4P, 4KPT, 4KQP, 4KR5, 4LA9

  • PubMed Abstract: 

    The ATP-binding cassette (ABC) transporter GlnPQ is an essential uptake system for amino acids in gram-positive pathogens and related nonpathogenic bacteria. The transporter has tandem substrate-binding domains (SBDs) fused to each transmembrane domain, giving rise to four SBDs per functional transporter complex. We have determined the crystal structures and ligand-binding properties of the SBDs of GlnPQ from Enterococcus faecalis, Streptococcus pneumoniae, and Lactococcus lactis. The tandem SBDs differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. The combined structural, functional, and thermodynamic analysis revealed the roles of individual residues in determining the substrate affinity. We succeeded in converting a low-affinity SBD into a high-affinity receptor and vice versa. Our data indicate that a small number of residues that reside in the binding pocket constitute the major affinity determinants of the SBDs.

  • Organizational Affiliation

    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine ABC transporter permease and substrate binding protein protein232Lactococcus lactis subsp. lactis Il1403Mutation(s): 0 
Gene Names: glnPL165LL1759
Find proteins for Q9CES5 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore Q9CES5 
Go to UniProtKB:  Q9CES5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CES5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GLN

Download Ideal Coordinates CCD File 
C5 H10 N2 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
GLN PDBBind:  4KQP Kd: 900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 0.95 Å
  • R-Value Free: 0.120 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.115 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.99α = 90
b = 51.69β = 91.1
c = 44.23γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations