PDBsum entry 2vda

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protein Protein-protein interface(s) links
Protein transport PDB id
Jmol PyMol
Protein chains
828 a.a. *
28 a.a. *
* Residue conservation analysis
PDB id:
Name: Protein transport
Title: Solution structure of the seca-signal peptide complex
Structure: Translocase subunit seca. Chain: a. Fragment: residues 9-836. Synonym: seca translocase atpase. Engineered: yes. Maltoporin. Chain: b. Fragment: signal sequence, residues 1-25. Synonym: maltose-inducible porin
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 562
NMR struc: 10 models
Authors: I.Gelis,A.M.J.J.Bonvin,D.Keramisanou,M.Koukaki,G.Gouridis, S.Karamanou,A.Economou,C.G.Kalodimos
Key ref:
I.Gelis et al. (2007). Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR. Cell, 131, 756-769. PubMed id: 18022369 DOI: 10.1016/j.cell.2007.09.039
01-Oct-07     Release date:   27-Nov-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P10408  (SECA_ECOLI) -  Protein translocase subunit SecA
901 a.a.
828 a.a.
Protein chain
Pfam   ArchSchema ?
Q8CVI4  (LAMB_ECOL6) -  Maltoporin
446 a.a.
28 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   6 terms 
  Biological process     chaperone-mediated protein folding   8 terms 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1016/j.cell.2007.09.039 Cell 131:756-769 (2007)
PubMed id: 18022369  
Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR.
I.Gelis, A.M.Bonvin, D.Keramisanou, M.Koukaki, G.Gouridis, S.Karamanou, A.Economou, C.G.Kalodimos.
Recognition of signal sequences by cognate receptors controls the entry of virtually all proteins to export pathways. Despite its importance, this process remains poorly understood. Here, we present the solution structure of a signal peptide bound to SecA, the 204 kDa ATPase motor of the Sec translocase. Upon encounter, the signal peptide forms an alpha-helix that inserts into a flexible and elongated groove in SecA. The mode of binding is bimodal, with both hydrophobic and electrostatic interactions mediating recognition. The same groove is used by SecA to recognize a diverse set of signal sequences. Impairment of the signal-peptide binding to SecA results in significant translocation defects. The C-terminal tail of SecA occludes the groove and inhibits signal-peptide binding, but autoinhibition is relieved by the SecB chaperone. Finally, it is shown that SecA interconverts between two conformations in solution, suggesting a simple mechanism for polypeptide translocation.
  Selected figure(s)  
Figure 3.
Figure 3. Structural Basis for Signal-Peptide Recognition by SecA
(A) The lowest-energy structure of SecA bound to the KRR-LamB signal peptide is shown. SecA is displayed as a semitransparent solvent-accessible surface, and the signal peptide is shown in yellow. A ribbon model is displayed below the surface (color code is as in Figure 1B).
(B) Closer view of the groove bound to the signal peptide. Green and red surface indicates hydrophobic and acidic residues, respectively. Peptide is shown as a ribbon ball-and-stick representation, and most of its residues are numbered.
(C) Contacts between the peptide (shown in yellow) and SecA residues. Electrostatic and hydrophobic interactions are indicated with red and green lines, respectively. SecA residues are colored according to the domain they are located at.
(D) A view of the groove bound to the signal peptide, wherein SecA is shown in ribbons. The peptide orientation is similar to that in (C). Dotted lines indicate electrostatic interactions between basic peptide residues and acidic SecA residues. Primed numbers indicate peptide residues.
Figure 6.
Figure 6. SecA Interconverts between an Open and Closed Conformation in Solution
(A) SecA shown in the so-called open (left) and closed (right) conformations. Interconversion between the two conformations requires that PBD undergo a vert, similar 60° rigid-body rotation (Osborne et al., 2004). PBD is displayed as semitransparent surface. The green sphere indicates residue 830, in which a paramagnetic spin label was introduced. Residues Ile304 and Ile789 are shown as yellow and red spheres, respectively. Characteristic distances in the two conformations are indicated. A strong NOE between Ile304 and Ile789 was observed, demonstrating that SecA adopts predominantly the open conformation in solution.
(B) Overlaid ^1H-^13C HMQC spectra of SecA bearing a spin label in position 830 in the reduced (blue) and oxidized (red) state. Residues that approach the spin label, even transiently, experience a broadening effect, which is suppressed in the reduced state.
  The above figures are reprinted from an Open Access publication published by Cell Press: Cell (2007, 131, 756-769) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23000954 M.E.Feltcher, and M.Braunstein (2012).
Emerging themes in SecA2-mediated protein export.
  Nat Rev Microbiol, 10, 779-789.  
21315086 A.J.Wowor, D.Yu, D.A.Kendall, and J.L.Cole (2011).
Energetics of SecA dimerization.
  J Mol Biol, 408, 87-98.  
21404360 C.G.Kalodimos (2011).
NMR reveals novel mechanisms of protein activity regulation.
  Protein Sci, 20, 773-782.  
21292166 D.Huber, N.Rajagopalan, S.Preissler, M.A.Rocco, F.Merz, G.Kramer, and B.Bukau (2011).
SecA interacts with ribosomes in order to facilitate posttranslational translocation in bacteria.
  Mol Cell, 41, 343-353.  
21234551 E.A.Kapellios, S.Karamanou, M.F.Sardis, M.Aivaliotis, A.Economou, and S.A.Pergantis (2011).
Using nanoelectrospray ion mobility spectrometry (GEMMA) to determine the size and relative molecular mass of proteins and protein assemblies: a comparison with MALLS and QELS.
  Anal Bioanal Chem, 399, 2421-2433.  
21183720 G.E.Karagöz, A.M.Duarte, H.Ippel, C.Uetrecht, T.Sinnige, M.van Rosmalen, J.Hausmann, A.J.Heck, R.Boelens, and S.G.Rüdiger (2011).
N-terminal domain of human Hsp90 triggers binding to the cochaperone p23.
  Proc Natl Acad Sci U S A, 108, 580-585.  
21435272 J.J.Minty, A.A.Lesnefsky, F.Lin, Y.Chen, T.A.Zaroff, A.B.Veloso, B.Xie, C.A.McConnell, R.J.Ward, D.R.Schwartz, J.M.Rouillard, Y.Gao, E.Gulari, and X.N.Lin (2011).
Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli.
  Microb Cell Fact, 10, 18.  
21360154 J.L.Gifford, H.Ishida, and H.J.Vogel (2011).
Fast methionine-based solution structure determination of calcium-calmodulin complexes.
  J Biomol NMR, 50, 71-81.
PDB code: 2l7l
21056980 K.Deville, V.A.Gold, A.Robson, S.Whitehouse, R.B.Sessions, S.A.Baldwin, S.E.Radford, and I.Collinson (2011).
The oligomeric state and arrangement of the active bacterial translocon.
  J Biol Chem, 286, 4659-4669.  
21337475 P.Palladino, G.Saviano, T.Tancredi, E.Benedetti, F.Rossi, and R.Ragone (2011).
Structural determinants of protein translocation in bacteria: conformational flexibility of SecA IRA1 loop region.
  J Pept Sci, 17, 263-269.  
21109422 S.R.Tzeng, and C.G.Kalodimos (2011).
Protein dynamics and allostery: an NMR view.
  Curr Opin Struct Biol, 21, 62-67.  
21062757 T.Didenko, R.Boelens, and S.G.Rüdiger (2011).
3D DOSY-TROSY to determine the translational diffusion coefficient of large protein complexes.
  Protein Eng Des Sel, 24, 99.  
21304597 Y.Tang, X.Pan, Y.Chen, P.C.Tai, and S.F.Sui (2011).
Dimeric SecA couples the preprotein translocation in an asymmetric manner.
  PLoS One, 6, e16498.  
20949307 A.M.Ruschak, A.Velyvis, and L.E.Kay (2010).
A simple strategy for ¹³C, ¹H labeling at the Ile-γ2 methyl position in highly deuterated proteins.
  J Biomol NMR, 48, 129-135.  
20734113 G.L.Butterfoss, E.F.DeRose, S.A.Gabel, L.Perera, J.M.Krahn, G.A.Mueller, X.Zheng, and R.E.London (2010).
Conformational dependence of 13C shielding and coupling constants for methionine methyl groups.
  J Biomol NMR, 48, 31-47.  
20593467 J.J.Bockhorn, K.L.Lazar, A.J.Gasser, L.M.Luther, I.M.Qahwash, N.Chopra, and S.C.Meredith (2010).
Novel semisynthetic method for generating full length beta-amyloid peptides.
  Biopolymers, 94, 511-520.  
21059946 L.Banci, I.Bertini, C.Cefaro, L.Cenacchi, S.Ciofi-Baffoni, I.C.Felli, A.Gallo, L.Gonnelli, E.Luchinat, D.Sideris, and K.Tokatlidis (2010).
Molecular chaperone function of Mia40 triggers consecutive induced folding steps of the substrate in mitochondrial protein import.
  Proc Natl Acad Sci U S A, 107, 20190-20195.
PDB code: 2l0y
21058670 R.Otten, J.Villali, D.Kern, and F.A.Mulder (2010).
Probing microsecond time scale dynamics in proteins by methyl (1)H Carr-Purcell-Meiboom-Gill relaxation dispersion NMR measurements. Application to activation of the signaling protein NtrC(r).
  J Am Chem Soc, 132, 17004-17014.  
20025247 S.M.Auclair, J.P.Moses, M.Musial-Siwek, D.A.Kendall, D.B.Oliver, and I.Mukerji (2010).
Mapping of the signal peptide-binding domain of Escherichia coli SecA using Förster resonance energy transfer.
  Biochemistry, 49, 782-792.  
20236317 S.Zakian, D.Lafitte, A.Vergnes, C.Pimentel, C.Sebban-Kreuzer, R.Toci, J.B.Claude, F.Guerlesquin, and A.Magalon (2010).
Basis of recognition between the NarJ chaperone and the N-terminus of the NarG subunit from Escherichia coli nitrate reductase.
  FEBS J, 277, 1886-1895.  
20360109 T.L.Religa, R.Sprangers, and L.E.Kay (2010).
Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR.
  Science, 328, 98.
PDB codes: 2ku1 2ku2
19361278 A.Kuhn (2009).
From the Sec complex to the membrane insertase YidC.
  Biol Chem, 390, 701-706.  
19273842 A.Robson, V.A.Gold, S.Hodson, A.R.Clarke, and I.Collinson (2009).
Energy transduction in protein transport and the ATP hydrolytic cycle of SecA.
  Proc Natl Acad Sci U S A, 106, 5111-5116.  
19363114 B.A.Bensing, and P.M.Sullam (2009).
Characterization of Streptococcus gordonii SecA2 as a paralogue of SecA.
  J Bacteriol, 191, 3482-3491.  
19933328 B.W.Bauer, and T.A.Rapoport (2009).
Mapping polypeptide interactions of the SecA ATPase during translocation.
  Proc Natl Acad Sci U S A, 106, 20800-20805.  
19450960 E.C.Mandon, S.F.Trueman, and R.Gilmore (2009).
Translocation of proteins through the Sec61 and SecYEG channels.
  Curr Opin Cell Biol, 21, 501-507.  
19924216 G.Gouridis, S.Karamanou, I.Gelis, C.G.Kalodimos, and A.Economou (2009).
Signal peptides are allosteric activators of the protein translocase.
  Nature, 462, 363-367.  
19359484 N.Popovych, S.R.Tzeng, M.Tonelli, R.H.Ebright, and C.G.Kalodimos (2009).
Structural basis for cAMP-mediated allosteric control of the catabolite activator protein.
  Proc Natl Acad Sci U S A, 106, 6927-6932.
PDB code: 2wc2
19288066 N.Sibille, X.Hanoulle, F.Bonachera, D.Verdegem, I.Landrieu, J.M.Wieruszeski, and G.Lippens (2009).
Selective backbone labelling of ILV methyl labelled proteins.
  J Biomol NMR, 43, 219-227.  
  20948662 S.R.Van Doren (2009).
Nuclear magnetic resonance captures the elusive.
  F1000 Biol Rep, 1, 0.  
19452133 W.Hwang, and M.J.Lang (2009).
Mechanical design of translocating motor proteins.
  Cell Biochem Biophys, 54, 11-22.  
18602400 D.B.Cooper, V.F.Smith, J.M.Crane, H.C.Roth, A.A.Lilly, and L.L.Randall (2008).
SecA, the motor of the secretion machine, binds diverse partners on one interactive surface.
  J Mol Biol, 382, 74-87.  
18421781 G.Thireos, G.Panayotou, and D.Thanos (2008).
Biochemistry and molecular biology research achievements in Greece.
  IUBMB Life, 60, 254-257.  
18613678 J.M.Hart, S.D.Kennedy, D.H.Mathews, and D.H.Turner (2008).
NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon.
  J Am Chem Soc, 130, 10233-10239.  
18923516 J.Zimmer, Y.Nam, and T.A.Rapoport (2008).
Structure of a complex of the ATPase SecA and the protein-translocation channel.
  Nature, 455, 936-943.
PDB codes: 3din 3dl8
18533288 N.C.Grassly, and C.Fraser (2008).
Mathematical models of infectious disease transmission.
  Nat Rev Microbiol, 6, 477-487.  
18761620 S.Karamanou, V.Bariami, E.Papanikou, C.G.Kalodimos, and A.Economou (2008).
Assembly of the translocase motor onto the preprotein-conducting channel.
  Mol Microbiol, 70, 311-322.  
18759741 X.Gatsos, A.J.Perry, K.Anwari, P.Dolezal, P.P.Wolynec, V.A.Likić, A.W.Purcell, S.K.Buchanan, and T.Lithgow (2008).
Protein secretion and outer membrane assembly in Alphaproteobacteria.
  FEMS Microbiol Rev, 32, 995.  
18772144 Y.Chen, X.Pan, Y.Tang, S.Quan, P.C.Tai, and S.F.Sui (2008).
Full-length Escherichia coli SecA dimerizes in a closed conformation in solution as determined by cryo-electron microscopy.
  J Biol Chem, 283, 28783-28787.  
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 code is shown on the right.