Crystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with cystine

Experimental Data Snapshot

  • Resolution: 1.56 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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Crystal structures of a putative periplasmic cystine-binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding.

Kumar, P.Kesari, P.Kokane, S.Ghosh, D.K.Kumar, P.Sharma, A.K.

(2019) FEBS J 286: 3450-3472

  • DOI: https://doi.org/10.1111/febs.14921
  • Primary Citation of Related Structures:  
    6A80, 6A8S, 6AA1, 6AAL

  • PubMed Abstract: 

    The amino acid-binding receptors, a component of ABC transporters, have evolved to cater to different specificities and functions. Of particular interest are cystine-binding receptors, which have shown broad specificity. In the present study, a putative periplasmic cystine-binding protein from Candidatus Liberibacter asiaticus (CLasTcyA) was characterized. Analysis of the CLasTcyA sequence and crystal structures in the ligand-bound state revealed novel features of CLasTcyA in comparison to related proteins. One of the unique features found in CLasTcyA structure was the positioning of the C-terminal extended loop of one chain very close to the substrate-binding site of the adjacent monomer in the asymmetric unit. The presence of a disulphide bond, unique to Candidatus Liberibacter family, holds the C-terminal extended loop in position. Analysis of the substrate-binding pocket of CLasTcyA suggested a broad specificity and a completely different orientation of the bound substrates in comparison to related protein structures. The open conformation for one of the two chains of the asymmetric unit in the Arg-bound structure revealed a limited open state (18.4°) for CLasTcyA as compared to open state of other related proteins (~ 60°). The strong interaction between Asp126 on helix-α5 of small domain and Arg82 (bigger domain) restricts the degree of opening in ligand-free open state. The dissociation constant of 1.26 μm by SPR and 3.7 μm by MST exhibited low affinity for the cystine. This is the first structural characterization of an l-cystine ABC transporter from plant pathogen and our results suggest that CLasTcyA may have evolved to cater to its specific needs for its survival in the host.

  • Organizational Affiliation

    Department of Biotechnology, Indian Institute of Technology Roorkee, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative amino acid-binding periplasmic ABC transporter protein
A, B
241Candidatus Liberibacter asiaticus str. psy62Mutation(s): 0 
Gene Names: CLIBASIA_05070
Find proteins for C6XGT2 (Liberibacter asiaticus (strain psy62))
Explore C6XGT2 
Go to UniProtKB:  C6XGT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6XGT2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TRS

Download Ideal Coordinates CCD File 
C4 H12 N O3
Query on CYS

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HA [auth B],
IA [auth B],
U [auth A],
V [auth A]
C3 H7 N O2 S
Query on GOL

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E [auth A],
FA [auth B],
Q [auth A],
R [auth A]
C3 H8 O3
Query on EDO

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AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
D [auth A]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
DA [auth B],
EA [auth B],
GA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
S [auth A],
T [auth A],
W [auth A],
X [auth A],
Y [auth B]
C2 H6 O2
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
Z [auth B]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.56 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.16α = 90
b = 86.78β = 90
c = 122.25γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
autoPROCdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description