X-ray structure of Brucella abortus RicA

Experimental Data Snapshot

  • Resolution: 2.73 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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This is version 1.2 of the entry. See complete history


Molecular Structure of the Brucella abortus Metalloprotein RicA, a Rab2-Binding Virulence Effector.

Herrou, J.Crosson, S.

(2013) Biochemistry 52: 9020-9028

  • DOI: https://doi.org/10.1021/bi401373r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Gram-negative intracellular pathogen Brucella abortus is the causative agent of brucellosis, which is among the most common zoonoses globally. The B. abortus RicA protein binds the host-expressed guanosine nucleotide-binding protein, Rab2, and modulates B. abortus infection biology. We have solved the first X-ray crystal structure of RicA to 2.7 Å resolution and have quantified the affinity of RicA binding to human Rab2 in its GDP-bound and nucleotide-free forms. RicA adopts a classic γ-carbonic anhydrase (γ-CA) fold containing a left-handed β-helix followed by a C-terminal α-helix. Two homotrimers of RicA occupy the crystallographic asymmetric unit. Though no zinc was included in the purification or crystallization buffers, zinc is contained within the RicA crystals, as demonstrated by X-ray fluorescence spectroscopy. Electron density for a Zn(2+) ion coordinated by three histidine residues is evident in the putative active site of RicA. However, purified RicA preparations do not exhibit carbonic anhydrase activity, suggesting that Zn(2+) may not be the physiologically relevant metal cofactor or that RicA is not a bona fide carbonic anhydrase enzyme. Isothermal titration calorimetry (ITC) measurements of purified RicA binding to purified human Rab2 and GDP-Rab2 revealed similar equilibrium affinities (Kd ≈ 35 and 40 μM, respectively). This study thus defines RicA as a Zn(2+)-binding γ-carbonic anhydrase-like protein that binds the human membrane fusion/trafficking protein Rab2 with low micromolar affinity in vitro. These results support a model in which γ-CA family proteins may evolve unique cellular functions while retaining many of the structural hallmarks of archetypal γ-CA enzymes.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 60637, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacterial transferase hexapeptide repeat
A, B, C, D, E
A, B, C, D, E, F
195Brucella abortus 2308Mutation(s): 0 
Gene Names: BAB1_1279BruAb1_1263
Find proteins for Q2YQG1 (Brucella abortus (strain 2308))
Explore Q2YQG1 
Go to UniProtKB:  Q2YQG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2YQG1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PE5

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
I [auth A],
L [auth C],
N [auth D],
P [auth E],
Q [auth E]
C18 H38 O9
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
J [auth B],
K [auth C],
M [auth D],
O [auth E],
R [auth F]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.43α = 90
b = 57.44β = 91.84
c = 127.61γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHENIXmodel building
xia2data reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-01-01
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Structure summary