4HCP

crystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis.

Yao, Q.Cui, J.Wang, J.Li, T.Wan, X.Luo, T.Gong, Y.N.Xu, Y.Huang, N.Shao, F.

(2012) Proc Natl Acad Sci U S A 109: 20395-20400

  • DOI: 10.1073/pnas.1210831109
  • Primary Citation of Related Structures:  
    4HCN, 4HCP

  • PubMed Abstract: 
  • Targeting eukaryotic proteins for deamidation modification is increasingly appreciated as a general bacterial virulence mechanism. Here, we present an atomic view of how a bacterial deamidase effector, cycle-inhibiting factor homolog in Burkholderia ...

    Targeting eukaryotic proteins for deamidation modification is increasingly appreciated as a general bacterial virulence mechanism. Here, we present an atomic view of how a bacterial deamidase effector, cycle-inhibiting factor homolog in Burkholderia pseudomallei (CHBP), recognizes its host targets, ubiquitin (Ub) and Ub-like neural precursor cell expressed, developmentally down-regulated 8 (NEDD8), and catalyzes site-specific deamidation. Crystal structures of CHBP-Ub/NEDD8 complexes show that Ub and NEDD8 are similarly cradled by a large cleft in CHBP with four contacting surfaces. The pattern of Ub/NEDD8 recognition by CHBP resembles that by the E1 activation enzyme, which critically involves the Lys-11 surface in Ub/NEDD8. Close examination of the papain-like catalytic center reveals structural determinants of CHBP being an obligate glutamine deamidase. Molecular-dynamics simulation identifies Gln-31/Glu-31 of Ub/NEDD8 as one key determinant of CHBP substrate preference for NEDD8. Inspired by the idea of using the unique bacterial activity as a tool, we further discover that CHBP-catalyzed NEDD8 deamidation triggers macrophage-specific apoptosis, which predicts a previously unknown macrophage-specific proapoptotic signal that is negatively regulated by neddylation-mediated protein ubiquitination/degradation.


    Organizational Affiliation

    College of Biological Sciences, China Agricultural University, Beijing 100094, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative ATP/GTP binding proteinA255Burkholderia pseudomallei K96243Mutation(s): 1 
Gene Names: BPSS1385
Find proteins for Q63KH5 (Burkholderia pseudomallei (strain K96243))
Explore Q63KH5 
Go to UniProtKB:  Q63KH5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8B78Homo sapiensMutation(s): 0 
Gene Names: NEDD8
Find proteins for Q15843 (Homo sapiens)
Explore Q15843 
Go to UniProtKB:  Q15843
NIH Common Fund Data Resources
PHAROS  Q15843
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.389α = 90
b = 44.973β = 110.83
c = 67.303γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-10-01 
  • Released Date: 2012-11-21 
  • Deposition Author(s): Yao, Q., Shao, F.

Revision History 

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references