PDBsum entry 1pyv

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Hydrolase PDB id
Protein chain
53 a.a.
PDB id:
Name: Hydrolase
Title: Nmr solution structure of the mitochondrial f1b presequence peptide from nicotiana plumbaginifolia
Structure: Atp synthase beta chain, mitochondrial precursor. Chain: a. Synonym: f1b presequence peptide. Engineered: yes
Source: Nicotiana plumbaginifolia. Curled-leaved tobacco. Organism_taxid: 4092. Gene: atpb or atp2-1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 24 models
Authors: P.Moberg,S.Nilsson,A.Stahl,A.C.Eriksson,E.Glaser,L.Maler
Key ref:
P.Moberg et al. (2004). NMR solution structure of the mitochondrial F1beta presequence from Nicotiana plumbaginifolia. J Mol Biol, 336, 1129-1140. PubMed id: 15037074 DOI: 10.1016/j.jmb.2004.01.006
09-Jul-03     Release date:   06-Apr-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P17614  (ATPBM_NICPL) -  ATP synthase subunit beta, mitochondrial
560 a.a.
53 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - H(+)-transporting two-sector ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + H+(In) = ADP + phosphate + H+(Out)
+ H(2)O
+ H(+)(In)
+ phosphate
+ H(+)(Out)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)   1 term 
  Biological process     ATP catabolic process   2 terms 
  Biochemical function     ATP binding     2 terms  


DOI no: 10.1016/j.jmb.2004.01.006 J Mol Biol 336:1129-1140 (2004)
PubMed id: 15037074  
NMR solution structure of the mitochondrial F1beta presequence from Nicotiana plumbaginifolia.
P.Moberg, S.Nilsson, A.Ståhl, A.C.Eriksson, E.Glaser, L.Mäler.
We have isolated, characterized and determined the three-dimensional NMR solution structure of the presequence of ATPsynthase F1beta subunit from Nicotiana plumbaginifolia. A general method for purification of presequences is presented. The method is based on overexpression of a mutant precursor containing a methionine residue introduced at the processing site, followed by CNBr-cleavage and purification of the presequence on a cation-exchange column. The F1beta presequence, 53 amino acid residues long, retained its native properties as evidenced by inhibition of in vitro mitochondrial import and processing at micromolar concentrations. CD spectroscopy revealed that the F1beta presequence formed an alpha-helical structure in membrane mimetic environments such as SDS and DPC micelles (approximately 50% alpha-helix), and in acidic phospholipid bicelles (approximately 60% alpha-helix). The NMR solution structure of the F1beta presequence in SDS micelles was determined on the basis of 518 distance and 21 torsion angle constraints. The structure was found to contain two helices, an N-terminal amphipathic alpha-helix (residues 4-15) and a C-terminal alpha-helix (residues 43-53), separated by a largely unstructured 27 residue long internal domain. The N-terminal amphipathic alpha-helix forms the putative Tom20 receptor binding site, whereas the C-terminal alpha-helix is located upstream of the mitochondrial processing peptidase cleavage site.
  Selected figure(s)  
Figure 8.
Figure 8. The effects of Mn2+ on HN-Ha peak-heights in TOCSY spectra mapped onto the representative F[1]b presequence structure. Dark blue color indicates residues for which peaks disappear at 1 mM Mn2+ and light blue color indicates residues for which peaks disappear at 2 mM Mn2+.
Figure 9.
Figure 9. Details in the structure of the F[1]b presequence peptide. A, The structure of the two helices with critical hydrophobic residues for forming the helical interface labeled; B, the structure of the N-terminal helix comprising residues Arg4-Gln15 with the side-chains of Arg4, Leu5, Leu6, Leu9, Leu10 and Arg11 labeled.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 336, 1129-1140) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20124346 T.Lithgow, and A.Schneider (2010).
Evolution of macromolecular import pathways in mitochondria, hydrogenosomes and mitosomes.
  Philos Trans R Soc Lond B Biol Sci, 365, 799-817.  
19703392 A.Chacinska, C.M.Koehler, D.Milenkovic, T.Lithgow, and N.Pfanner (2009).
Importing mitochondrial proteins: machineries and mechanisms.
  Cell, 138, 628-644.  
19995731 A.K.Berglund, E.Spånning, H.Biverståhl, G.Maddalo, C.Tellgren-Roth, L.Mäler, and E.Glaser (2009).
Dual Targeting to Mitochondria and Chloroplasts: Characterization of Thr-tRNA Synthetase Targeting Peptide.
  Mol Plant, 2, 1298-1309.  
19701724 S.Nilsson Cederholm, H.G.Bäckman, P.Pesaresi, D.Leister, and E.Glaser (2009).
Deletion of an organellar peptidasome PreP affects early development in Arabidopsis thaliana.
  Plant Mol Biol, 71, 497-508.  
18392626 J.Rokov-Plavec, M.Dulic, A.M.Duchêne, and I.Weygand-Durasevic (2008).
Dual targeting of organellar seryl-tRNA synthetase to maize mitochondria and chloroplasts.
  Plant Cell Rep, 27, 1157-1168.  
17081117 E.Glaser, S.Nilsson, and S.Bhushan (2006).
Two novel mitochondrial and chloroplastic targeting-peptide-degrading peptidasomes in A. thaliana, AtPreP1 and AtPreP2.
  Biol Chem, 387, 1441-1447.  
17073452 S.Abu-Baker, and G.A.Lorigan (2006).
Phospholamban and its phosphorylated form interact differently with lipid bilayers: a 31P, 2H, and 13C solid-state NMR spectroscopic study.
  Biochemistry, 45, 13312-13322.  
17105808 T.Salinas, A.M.Duchêne, L.Delage, S.Nilsson, E.Glaser, M.Zaepfel, and L.Maréchal-Drouard (2006).
The voltage-dependent anion channel, a major component of the tRNA import machinery in plant mitochondria.
  Proc Natl Acad Sci U S A, 103, 18362-18367.  
15803408 M.D.Shih, S.C.Lin, J.S.Hsieh, C.H.Tsou, T.Y.Chow, T.P.Lin, and Y.I.Hsing (2004).
Gene cloning and characterization of a soybean (Glycine max L.) LEA protein, GmPM16.
  Plant Mol Biol, 56, 689-703.  
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.