7DPY | pdb_00007dpy

Structure of Brucella abortus PhiA

• PDB DOI: https://doi.org/10.2210/pdb7DPY/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Brucella abortus bv. 1 str. 9-941
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-22 Released: 2021-06-23 
• Deposition Author(s): Hyun, Y., Ha, N.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.231 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structure and Function of the Autolysin SagA in the Type IV Secretion System of Brucella abortus .

Hyun, Y., Baek, Y., Lee, C., Ki, N., Ahn, J., Ryu, S., Ha, N.C.

(2021) Mol Cells 44: 517-528

• PubMed: 34112742 
• DOI: https://doi.org/10.14348/molcells.2021.0011
• Primary Citation Related Structures: 
  7DNP, 7DPY


• PubMed Abstract: 
  

  A recent genetic study with Brucella abortus revealed the secretion activator gene A (SagA) as an autolysin component creating pores in the peptidoglycan (PGN) layer for the type IV secretion system (T4SS) and peptidoglycan hydrolase inhibitor A (PhiA) as an inhibitor of SagA. In this study, we determined the crystal structures of both SagA and PhiA. Notably, the SagA structure contained a PGN fragment in a space between the N- and C-terminal domains, showing the substrate-dependent hinge motion of the domains. The purified SagA fully hydrolyzed the meso-diaminopimelic acid (DAP)-type PGN, showing a higher activity than hen egg-white lysozyme. The PhiA protein exhibiting tetrameric assembly failed to inhibit SagA activity in our experiments. Our findings provide implications for the molecular basis of the SagA-PhiA system of B. abortus . The development of inhibitors of SagA would further contribute to controlling brucellosis by attenuating the function of T4SS, the major virulence factor of Brucella .

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Organizational Affiliation: 
• Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, CALS, Seoul National University, Seoul 08826, Korea.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 24.54 kDa 
• Atom Count: 1,511 
• Modeled Residue Count: 179 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Brucella Abortus PhiA	A, B	109	Brucella abortus bv. 1 str. 9-941	Mutation(s): 0  Gene Names: BruAb1_0102
UniProt
Find proteins for Q57FR6 (Brucella abortus biovar 1 (strain 9-941)) Explore Q57FR6  Go to UniProtKB:  Q57FR6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.231 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.155	α = 90
b = 51.156	β = 90
c = 62.303	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Hyun, Y., Ha, N.-C.

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2021-08-11
  Changes: Database references
• Version 1.2: 2021-10-13
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary