5ZXA

Crystal structure of fibronectin-binding protein Apa mutant from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Functional and structural investigations of fibronectin-binding protein Apa from Mycobacterium tuberculosis.

Kuo, C.J.Gao, J.Huang, J.W.Ko, T.P.Zhai, C.Ma, L.Liu, W.Dai, L.Chang, Y.F.Chen, T.H.Hu, Y.Yu, X.Guo, R.T.Chen, C.C.

(2019) Biochim Biophys Acta Gen Subj 1863: 1351-1359

  • DOI: https://doi.org/10.1016/j.bbagen.2019.06.003
  • Primary Citation of Related Structures:  
    5ZX9, 5ZXA

  • PubMed Abstract: 

    Alanine and proline-rich protein (Apa) is a secreted antigen of Mycobacterium spp. which involves in stimulating immune responses and adhering to host cells by binding to fibronectin (Fn). Here, we report the crystal structure of Apa from Mycobacterium tuberculosis (Mtb) and its Fn-binding characteristics. The crystal structure of Mtb Apa was determined at resolutions of 1.54 Å. The dissociation constants (K D ) of Apa and individual modules of Fn were determined by surface plasmon resonance and enzyme-linked immunosorbent assay. Site-directed mutagenesis was performed to investigate the putative Fn-binding motif of Apa. Mtb Apa folds into a large seven-stranded anti-parallel β-sheet which is flanked by three α-helices. The binding affinity of Mtb Apa to individual Fn modules was assessed and the results indicated that the Mtb Apa binds to FnIII-4 and FnIII-5 of Fn CBD segment. Notably, structure analysis suggested that the previously proposed Fn-binding motif 258 RWFV 261 is buried within the protein and may not be accessible to the binding counterpart. The structural and Fn-binding characteristics we reported here provide molecular insights into the multifunctional protein Mtb Apa. FnIII-4 and FnIII-5 of CBD are the only two modules contributing to Apa-Fn interaction. This is the first study to report the structure and Fn-binding characteristics of mycobacterial Apa. Since Apa plays a central role in stimulating immune responses and host cells adhesion, these results are of great importance in understanding the pathogenesis of mycobacterium. This information shall provide a guidance for the development of anti-mycobacteria regimen.


  • Organizational Affiliation

    Department of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alanine and proline-rich secreted protein Apa325Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: 1860c
UniProt
Find proteins for P9WIR7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIR7 
Go to UniProtKB:  P9WIR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WIR7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.028α = 90
b = 118.028β = 90
c = 118.852γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references, Structure summary
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references