4H03

Crystal structure of NAD+-Ia-actin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex

Tsurumura, T.Tsumori, Y.Qiu, H.Oda, M.Sakurai, J.Nagahama, M.Tsuge, H.

(2013) Proc Natl Acad Sci U S A 110: 4267-4272

  • DOI: 10.1073/pnas.1217227110
  • Primary Citation of Related Structures:  
    4GY2, 4H03, 4H0T, 4H0V, 4H0X, 4H0Y

  • PubMed Abstract: 
  • Clostridium perfringens iota-toxin (Ia) mono-ADP ribosylates Arg177 of actin, leading to cytoskeletal disorganization and cell death. To fully understand the reaction mechanism of arginine-specific mono-ADP ribosyl transferase, the structure of the toxin-substrate protein complex must be characterized ...

    Clostridium perfringens iota-toxin (Ia) mono-ADP ribosylates Arg177 of actin, leading to cytoskeletal disorganization and cell death. To fully understand the reaction mechanism of arginine-specific mono-ADP ribosyl transferase, the structure of the toxin-substrate protein complex must be characterized. Recently, we solved the crystal structure of Ia in complex with actin and the nonhydrolyzable NAD(+) analog βTAD (thiazole-4-carboxamide adenine dinucleotide); however, the structures of the NAD(+)-bound form (NAD(+)-Ia-actin) and the ADP ribosylated form [Ia-ADP ribosylated (ADPR)-actin] remain unclear. Accidentally, we found that ethylene glycol as cryo-protectant inhibits ADP ribosylation and crystallized the NAD(+)-Ia-actin complex. Here we report high-resolution structures of NAD(+)-Ia-actin and Ia-ADPR-actin obtained by soaking apo-Ia-actin crystal with NAD(+) under different conditions. The structures of NAD(+)-Ia-actin and Ia-ADPR-actin represent the pre- and postreaction states, respectively. By assigning the βTAD-Ia-actin structure to the transition state, the strain-alleviation model of ADP ribosylation, which we proposed previously, is experimentally confirmed and improved. Moreover, this reaction mechanism appears to be applicable not only to Ia but also to other ADP ribosyltransferases.


    Organizational Affiliation

    Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Iota toxin component IaA418Clostridium perfringensMutation(s): 0 
EC: 2.4.2.31
Find proteins for Q46220 (Clostridium perfringens)
Explore Q46220 
Go to UniProtKB:  Q46220
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Actin, alpha skeletal muscleB375Oryctolagus cuniculusMutation(s): 0 
Gene Names: ACTA1ACTA
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
ATP
Query on ATP

Download Ideal Coordinates CCD File 
CA [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
LAR
Query on LAR

Download Ideal Coordinates CCD File 
DA [auth B]LATRUNCULIN A
C22 H31 N O5 S
DDVBPZROPPMBLW-IZGXTMSKSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

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AA [auth A] , AB [auth B] , BB [auth B] , CB [auth B] , E [auth A] , EA [auth B] , F [auth A] , FA [auth B] , 
AA [auth A],  AB [auth B],  BB [auth B],  CB [auth B],  E [auth A],  EA [auth B],  F [auth A],  FA [auth B],  G [auth A],  GA [auth B],  H [auth A],  HA [auth B],  I [auth A],  IA [auth B],  J [auth A],  JA [auth B],  K [auth A],  KA [auth B],  L [auth A],  LA [auth B],  M [auth A],  MA [auth B],  N [auth A],  NA [auth B],  O [auth A],  OA [auth B],  P [auth A],  PA [auth B],  Q [auth A],  QA [auth B],  R [auth A],  RA [auth B],  S [auth A],  SA [auth B],  T [auth A],  TA [auth B],  U [auth A],  UA [auth B],  V [auth A],  VA [auth B],  W [auth A],  WA [auth B],  X [auth A],  XA [auth B],  Y [auth A],  YA [auth B],  Z [auth A],  ZA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HIC
Query on HIC
BL-PEPTIDE LINKINGC7 H11 N3 O2HIS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LARIC50:  40   nM  BindingDB
LARIC50:  70   nM  BindingDB
LARIC50:  110   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.862α = 90
b = 135.037β = 90
c = 154.51γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references