3DSG

XC1028 from Xanthomonas campestris Adopts a PilZ Domain-like Structure Yet with Trivial c-di-GMP Binding Activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

XC1028 from Xanthomonas campestris adopts a PilZ domain-like structure without a c-di-GMP switch.

Li, T.N.Chin, K.H.Liu, J.H.Wang, A.H.Chou, S.H.

(2009) Proteins 75: 282-288

  • DOI: 10.1002/prot.22330
  • Primary Citation of Related Structures:  
    3DSG

  • PubMed Abstract: 
  • The crystal structure of XC1028 from Xanthomonas campestris has been determined to a resolution of 2.15 A using the multiple anomalous dispersion approach. It bears significant sequence identity and similarity values of 64.10% and 70.09%, respectively, with PA2960, a protein indispensable for type IV pilus-mediated twitching motility, after which the PilZ motif was first named ...

    The crystal structure of XC1028 from Xanthomonas campestris has been determined to a resolution of 2.15 A using the multiple anomalous dispersion approach. It bears significant sequence identity and similarity values of 64.10% and 70.09%, respectively, with PA2960, a protein indispensable for type IV pilus-mediated twitching motility, after which the PilZ motif was first named. However, both XC1028 and PA2960 lack detectable c-di-GMP binding capability. Although XC1028 adopts a structure comprising a five-stranded beta-barrel core similar to other canonical PilZ domains with robust c-di-GMP binding ability, considerable differences are observed in the N-terminal motif; XC1028 assumes a compact five-stranded beta-barrel without an extra long N-terminal motif, whereas other canonical PilZ domains contain a long N-terminal sequence embedded with an essential "c-di-GMP switch" motif. In addition, a beta-strand (beta1) in the N-terminal motif, running in exactly opposite polarity to that of XC1028, is found inserted into the parallel beta3/beta1' strands, forming a completely antiparallel beta4 downward arrow beta3 upward arrow beta1 downward arrow beta1' upward arrow sheet in the canonical PilZ domains. Such dramatic structural differences at the N-terminus may account for the diminished c-di-GMP binding capability of XC1028, and suggest that interactions with additional proteins are necessary to bind c-di-GMP for type IV fimbriae assembly.


    Organizational Affiliation

    Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227, Taiwan, Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Type IV fimbriae assembly proteinA, B, C99Xanthomonas campestris pv. campestrisMutation(s): 0 
Find proteins for Q8PBU4 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25))
Explore Q8PBU4 
Go to UniProtKB:  Q8PBU4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.896α = 90
b = 50.962β = 90.21
c = 92.745γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance