5B7W

Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv.campestris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris

Zhao, Z.Wu, Z.Zhang, J.

(2016) Acta Crystallogr F Struct Biol Commun 72: 720-725

  • DOI: https://doi.org/10.1107/S2053230X16013017
  • Primary Citation of Related Structures:  
    5B7W

  • PubMed Abstract: 

    As an important bacterial second messenger, bis-(3',5')-cyclic diguanylate (cyclic di-GMP or c-di-GMP) has been implicated in numerous biological activities, including biofilm formation, motility, survival and virulence. These processes are manipulated by the binding of c-di-GMP to its receptors. XC_3703 from the plant pathogen Xanthomonas campestris pv. campestris, which belongs to the YajQ family of proteins, has recently been identified as a potential c-di-GMP receptor. XC_3703, together with XC_2801, functions as a transcription factor activating virulence-related genes, which can be reversed by the binding of c-di-GMP to XC_3703. However, the structural basis of how c-di-GMP regulates XC_3703 remains elusive. In this study, the structure of XC_3703 was determined to 2.1 Å resolution using the molecular-replacement method. The structure of XC_3703 consists of two domains adopting the same topology, which is similar to that of the RNA-recognition motif (RRM). Arg65, which is conserved among the c-di-GMP-binding subfamily of the YajQ family of proteins, together with Phe80 in domain II, forms a putative c-di-GMP binding site.


  • Organizational Affiliation

    College of Biology, Pharmacy and Food Engineering, Shangluo University, Shangluo 726000, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0234 protein XC_3703
A, B
169Xanthomonas campestris pv. campestris str. 8004Mutation(s): 0 
Gene Names: XC_3703
UniProt
Find proteins for Q4UQD0 (Xanthomonas campestris pv. campestris (strain 8004))
Explore Q4UQD0 
Go to UniProtKB:  Q4UQD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4UQD0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.51α = 90
b = 65.47β = 92.69
c = 52.284γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations