4N27 | pdb_00004n27

X-ray structure of Brucella abortus RicA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 
    0.255 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4N27

This is version 1.2 of the entry. See complete history

Literature

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 Related Structures: 
    4N27

  • 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.

Macromolecule Content 

  • Total Structure Weight: 127.49 kDa 
  • Atom Count: 7,977 
  • Modeled Residue Count: 1,050 
  • Deposited Residue Count: 1,170 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
UniProt
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE5

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]
3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
C18 H38 O9
CUDPPTPIUWYGFI-UHFFFAOYSA-N
ZN

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]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 1 21 1
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
PHENIXrefinement
xia2data reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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