4KR5

Crystal structure of Lactococcus lactis GlnP substrate binding domain 2 (SBD2) in open conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine ABC transporter permease and substrate binding protein protein
A, B
232Lactococcus lactis subsp. lactis Il1403Mutation(s): 0 
Gene Names: glnPL165LL1759
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download Ideal Coordinates CCD File 
M [auth B]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
P33
Query on P33

Download Ideal Coordinates CCD File 
N [auth B]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
P6G
Query on P6G

Download Ideal Coordinates CCD File 
G [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PG0
Query on PG0

Download Ideal Coordinates CCD File 
L [auth B]2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B],
J [auth B],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.691α = 90
b = 89.123β = 95.58
c = 59.477γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata 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, Structure summary