4ITR

Crystal Structure of IbpAFic2-H3717A in complex with adenylylated Cdc42


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis of Fic-mediated adenylylation.

Xiao, J.Worby, C.A.Mattoo, S.Sankaran, B.Dixon, J.E.

(2010) Nat Struct Mol Biol 17: 1004-1010

  • DOI: 10.1038/nsmb.1867
  • Primary Citation of Related Structures:  
    4ITR, 3N3U

  • PubMed Abstract: 
  • The Fic family of adenylyltransferases, defined by a core HPFx(D/E)GN(G/K)R motif, consists of over 2,700 proteins found in organisms from bacteria to humans. The immunoglobulin-binding protein A (IbpA) from the bacterial pathogen Histophilus somni contains two Fic domains that adenylylate the switch1 tyrosine residue of Rho-family GTPases, allowing the bacteria to subvert host defenses ...

    The Fic family of adenylyltransferases, defined by a core HPFx(D/E)GN(G/K)R motif, consists of over 2,700 proteins found in organisms from bacteria to humans. The immunoglobulin-binding protein A (IbpA) from the bacterial pathogen Histophilus somni contains two Fic domains that adenylylate the switch1 tyrosine residue of Rho-family GTPases, allowing the bacteria to subvert host defenses. Here we present the structure of the second Fic domain of IbpA (IbpAFic2) in complex with its substrate, Cdc42. IbpAFic2-bound Cdc42 mimics the GDI-bound state of Rho GTPases, with both its switch1 and switch2 regions gripped by IbpAFic2. Mutations disrupting the IbpAFic2-Cdc42 interface impair adenylylation and cytotoxicity. Notably, the switch1 tyrosine of Cdc42 is adenylylated in the structure, providing the first structural view for this post-translational modification. We also show that the nucleotide-binding mechanism is conserved among Fic proteins and propose a catalytic mechanism for this recently discovered family of enzymes.


    Organizational Affiliation

    Department of Pharmacology, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenosine monophosphate-protein transferase and cysteine protease IbpA AB316Histophilus somni 2336Mutation(s): 1 
Gene Names: ibpAp76HSM_1489
EC: 2.7.7.1 (PDB Primary Data), 2.7.7 (UniProt), 3.4.22 (UniProt)
Find proteins for Q06277 (Histophilus somni (strain 2336))
Explore Q06277 
Go to UniProtKB:  Q06277
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 42 homolog CD191Homo sapiensMutation(s): 0 
Gene Names: CDC42
EC: 3.6.5.2
Find proteins for P60953 (Homo sapiens)
Explore P60953 
Go to UniProtKB:  P60953
NIH Common Fund Data Resources
PHAROS:  P60953
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.495α = 90
b = 90.997β = 90
c = 190.969γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-01-18 
  • Released Date: 2013-02-20 
  • Deposition Author(s): Xiao, J., Dixon, J.E.
  • This entry supersedes: 3N3V

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release