3BB1

Crystal structure of Toc34 from Pisum sativum in complex with Mg2+ and GMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The GTPase cycle of the chloroplast import receptors Toc33/Toc34: implications from monomeric and dimeric structures.

Koenig, P.Oreb, M.Hofle, A.Kaltofen, S.Rippe, K.Sinning, I.Schleiff, E.Tews, I.

(2008) Structure 16: 585-596

  • DOI: 10.1016/j.str.2008.01.008
  • Primary Citation of Related Structures:  
    3BB1, 3BB3, 3BB4

  • PubMed Abstract: 
  • Transport of precursor proteins across chloroplast membranes involves the GTPases Toc33/34 and Toc159 at the outer chloroplast envelope. The small GTPase Toc33/34 can homodimerize, but the regulation of this interaction has remained elusive. We show that dimerization is independent of nucleotide loading state, based on crystal structures of dimeric Pisum sativum Toc34 and monomeric Arabidopsis thaliana Toc33 ...

    Transport of precursor proteins across chloroplast membranes involves the GTPases Toc33/34 and Toc159 at the outer chloroplast envelope. The small GTPase Toc33/34 can homodimerize, but the regulation of this interaction has remained elusive. We show that dimerization is independent of nucleotide loading state, based on crystal structures of dimeric Pisum sativum Toc34 and monomeric Arabidopsis thaliana Toc33. An arginine residue is--in the dimer--positioned to resemble a GAP arginine finger. However, GTPase activation by dimerization is sparse and active site features do not explain catalysis, suggesting that the homodimer requires an additional factor as coGAP. Access to the catalytic center and an unusual switch I movement in the dimeric structure support this finding. Potential binding sites for interactions within the Toc translocon or with precursor proteins can be derived from the structures.


    Organizational Affiliation

    Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Translocase of chloroplast 34
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
274Pisum sativumMutation(s): 1 
Gene Names: TOC34IAP34OEP34
EC: 3.6.5
UniProt
Find proteins for Q41009 (Pisum sativum)
Explore Q41009 
Go to UniProtKB:  Q41009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ41009
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
BA [auth G],
FA [auth H],
J [auth A],
N [auth B],
P [auth C],
BA [auth G],
FA [auth H],
J [auth A],
N [auth B],
P [auth C],
S [auth D],
U [auth E],
X [auth F]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
K [auth A],
Y [auth F]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth G],
DA [auth G],
L [auth A],
Q [auth C],
V [auth E],
CA [auth G],
DA [auth G],
L [auth A],
Q [auth C],
V [auth E],
Z [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth G],
EA [auth H],
I [auth A],
M [auth B],
O [auth C],
AA [auth G],
EA [auth H],
I [auth A],
M [auth B],
O [auth C],
R [auth D],
T [auth E],
W [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GNP PDBBind:  3BB1 Kd: 2.50e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.776α = 90
b = 180.061β = 90
c = 90.948γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DNAdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations