4ITR

Crystal Structure of IbpAFic2-H3717A in complex with adenylylated Cdc42


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 

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:  

  • 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 c ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosine monophosphate-protein transferase and cysteine protease IbpA
A, B
316Histophilus somni (strain 2336)Mutation(s): 1 
Gene Names: ibpA (p76)
Find proteins for Q06277 (Histophilus somni (strain 2336))
Go to UniProtKB:  Q06277
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cell division control protein 42 homolog
C, D
191Homo sapiensMutation(s): 0 
Gene Names: CDC42
Find proteins for P60953 (Homo sapiens)
Go to Gene View: CDC42
Go to UniProtKB:  P60953
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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Download CCD File 
C, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

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Download CCD File 
C, D
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.495α = 90.00
b = 90.997β = 90.00
c = 190.969γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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