4XSH

The complex structure of C3cer exoenzyme and GTP bound RhoA (NADH-bound state)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rho GTPase Recognition by C3 Exoenzyme Based on C3-RhoA Complex Structure.

Toda, A.Tsurumura, T.Yoshida, T.Tsumori, Y.Tsuge, H.

(2015) J.Biol.Chem. 290: 19423-19432

  • DOI: 10.1074/jbc.M115.653220
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • C3 exoenzyme is a mono-ADP-ribosyltransferase (ART) that catalyzes transfer of an ADP-ribose moiety from NAD(+) to Rho GTPases. C3 has long been used to study the diverse regulatory functions of Rho GTPases. How C3 recognizes its substrate and how AD ...

    C3 exoenzyme is a mono-ADP-ribosyltransferase (ART) that catalyzes transfer of an ADP-ribose moiety from NAD(+) to Rho GTPases. C3 has long been used to study the diverse regulatory functions of Rho GTPases. How C3 recognizes its substrate and how ADP-ribosylation proceeds are still poorly understood. Crystal structures of C3-RhoA complex reveal that C3 recognizes RhoA via the switch I, switch II, and interswitch regions. In C3-RhoA(GTP) and C3-RhoA(GDP), switch I and II adopt the GDP and GTP conformations, respectively, which explains why C3 can ADP-ribosylate both nucleotide forms. Based on structural information, we successfully changed Cdc42 to an active substrate with combined mutations in the C3-Rho GTPase interface. Moreover, the structure reflects the close relationship among Gln-183 in the QXE motif (C3), a modified Asn-41 residue (RhoA) and NC1 of NAD(H), which suggests that C3 is the prototype ART. These structures show directly for the first time that the ARTT loop is the key to target protein recognition, and they also serve to bridge the gaps among independent studies of Rho GTPases and C3.


    Organizational Affiliation

    From the Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, and the Structural Biology Research Center, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan tsuge@cc.kyoto-su.ac.jp.,From the Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, and.,From the Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, and the Structural Biology Research Center, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transforming protein RhoA
A
179Homo sapiensMutation(s): 1 
Gene Names: RHOA (ARH12, ARHA, RHO12)
EC: 3.6.5.2
Find proteins for P61586 (Homo sapiens)
Go to Gene View: RHOA
Go to UniProtKB:  P61586
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosyltransferase
B
219Bacillus cereusMutation(s): 0 
Gene Names: c3cer
Find proteins for Q8KNY0 (Bacillus cereus)
Go to UniProtKB:  Q8KNY0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAI
Query on NAI

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Download CCD File 
B
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
GSP
Query on GSP

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Download CCD File 
A
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.190 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 50.424α = 90.00
b = 50.424β = 90.00
c = 136.667γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grants-in-Aid for Scientific Research, MEXT of JapanJapan25121733

Revision History 

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-08-19
    Type: Database references