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PDBsum entry 3bb4
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Hydrolase PDB id
3bb4

 

 

 

 

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Contents
Protein chain
240 a.a. *
Ligands
GNP
Metals
_MG
Waters ×27
* Residue conservation analysis
PDB id:
3bb4
Name: Hydrolase
Title: Crystal structure of toc33 from arabidopsis thaliana in complex with mg2+ and gmppnp
Structure: T7i23.11 protein. Chain: a. Fragment: unp residues 1-251. Synonym: at1g02280, at1g02280/t7i23.11, attoc33 protein. Engineered: yes. Mutation: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Strain: columbia. Gene: t7i23.11. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.85Å     R-factor:   0.221     R-free:   0.277
Authors: P.Koenig,I.Sinning,E.Schleiff,I.Tews
Key ref:
P.Koenig et al. (2008). The GTPase cycle of the chloroplast import receptors Toc33/Toc34: implications from monomeric and dimeric structures. Structure, 16, 585-596. PubMed id: 18400179 DOI: 10.1016/j.str.2008.01.008
Date:
09-Nov-07     Release date:   01-Apr-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O23680  (TOC33_ARATH) -  Translocase of chloroplast 33, chloroplastic from Arabidopsis thaliana
Seq:
Struc: 		297 a.a.
240 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.6.5.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.str.2008.01.008 Structure 16:585-596 (2008)
PubMed id: 18400179  
 
 
The GTPase cycle of the chloroplast import receptors Toc33/Toc34: implications from monomeric and dimeric structures.
P.Koenig, M.Oreb, A.Höfle, S.Kaltofen, K.Rippe, I.Sinning, E.Schleiff, I.Tews.
 
  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. 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.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Comparison of the G3 Regions in psToc34 and Ras p21
(A) The conformation of G3/switch II is identical in the GMPPNP- and the GDP-bound states of psToc34. Gly96 is in hydrogen-bonding distance to the γ-phosphate, and is conserved in the GTPase G3 motif (DxxG). Leu97, directly following the G3 motif, enters a hydrophobic pocket between helices α2 and α3.
(B) A similar representation as in (A) for G3/switch II of Ras p21 (PDB code: 5P21) (Pai et al., 1990). Gly60 is in hydrogen-bonding distance to the γ-phosphate in the GMPPNP-bound state; different from psToc34, Gly60 is turned away from the binding pocket in the GDP-bound state of Ras p21 (not shown). The equivalent residue to Leu97 of psToc34 is the catalytic residue Gln61 in Ras p21, which is turned toward the nucleotide.
(C) The alignment shows the G3 region of six members of the Aig1/Toc34/Toc159-like paraseptin GTPase family, together with three GTPases of the TRAFAC class. 		Figure 5.
Figure 5. Glu73 of G2/Switch I Senses the Nucleotide Loading State in Dimeric psToc34
(A) psGlu73 is solvent exposed in psToc34 in the GMPPNP-bound state. A water that might be in position for nucleophilic attack on the γ-phosphate is shown as a small blue sphere. The water is in hydrogen-bonding distance to Gly74 of the G2 region.
(B) In the GDP-bound state (PDB code: 1H65) (Sun et al., 2002), psGlu73 is turned toward the nucleotide and takes the position of the γ-phosphate. It then coordinates the Mg^2+ ion.
 
  The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 585-596) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20192748 H.M.Li, and C.C.Chiu (2010).
Protein transport into chloroplasts.
  Annu Rev Plant Biol, 61, 157-180.  
20123128 K.W.Hung, Y.W.Chang, E.T.Eng, J.H.Chen, Y.C.Chen, Y.J.Sun, C.D.Hsiao, G.Dong, K.A.Spasov, V.M.Unger, and T.H.Huang (2010).
Structural fold, conservation and Fe(II) binding of the intracellular domain of prokaryote FeoB.
  J Struct Biol, 170, 501-512.
PDB codes: 2wia 2wib 2wic 3k53
19187236 B.Agne, and F.Kessler (2009).
Protein transport in organelles: The Toc complex way of preprotein import.
  FEBS J, 276, 1156-1165.  
19188370 B.Agne, S.Infanger, F.Wang, V.Hofstetter, G.Rahim, M.Martin, D.W.Lee, I.Hwang, D.Schnell, and F.Kessler (2009).
A toc159 import receptor mutant, defective in hydrolysis of GTP, supports preprotein import into chloroplasts.
  J Biol Chem, 284, 8670-8679.  
19410443 F.Kessler, and D.Schnell (2009).
Chloroplast biogenesis: diversity and regulation of the protein import apparatus.
  Curr Opin Cell Biol, 21, 494-500.  
19010773 G.Rahim, S.Bischof, F.Kessler, and B.Agne (2009).
In vivo interaction between atToc33 and atToc159 GTP-binding domains demonstrated in a plant split-ubiquitin system.
  J Exp Bot, 60, 257-267.  
19744928 J.Lee, F.Wang, and D.J.Schnell (2009).
Toc receptor dimerization participates in the initiation of membrane translocation during protein import into chloroplasts.
  J Biol Chem, 284, 31130-31141.  
19335200 M.S.Sommer, and E.Schleiff (2009).
Molecular interactions within the plant TOC complex.
  Biol Chem, 390, 739-744.  
19805342 M.Sirajuddin, M.Farkasovsky, E.Zent, and A.Wittinghofer (2009).
GTP-induced conformational changes in septins and implications for function.
  Proc Natl Acad Sci U S A, 106, 16592-16597.
PDB code: 3ftq
19424291 R.Gasper, S.Meyer, K.Gotthardt, M.Sirajuddin, and A.Wittinghofer (2009).
It takes two to tango: regulation of G proteins by dimerization.
  Nat Rev Mol Cell Biol, 10, 423-429.  
19806182 S.Meyer, S.Böhme, A.Krüger, H.J.Steinhoff, J.P.Klare, and A.Wittinghofer (2009).
Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy.
  PLoS Biol, 7, e1000212.
PDB codes: 3gee 3geh 3gei
18541539 P.Koenig, M.Oreb, K.Rippe, C.Muhle-Goll, I.Sinning, E.Schleiff, and I.Tews (2008).
On the significance of Toc-GTPase homodimers.
  J Biol Chem, 283, 23104-23112.
PDB code: 3def
19001421 T.Bionda, P.Koenig, M.Oreb, I.Tews, and E.Schleiff (2008).
pH sensitivity of the GTPase Toc33 as a regulatory circuit for protein translocation into chloroplasts.
  Plant Cell Physiol, 49, 1917-1921.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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