spacer
spacer

PDBsum entry 1tf2
Go to PDB code: 
protein ligands metals links
Protein transport PDB id
1tf2

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
772 a.a. *
Ligands
ADP
Metals
_MG
Waters ×26
* Residue conservation analysis
PDB id:
1tf2
Name: Protein transport
Title: Crystal structure of seca:adp in an open conformation from bacillus subtilis
Structure: Preprotein translocase seca subunit. Chain: a. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: seca, div+, bsu35300. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.90Å     R-factor:   0.228     R-free:   0.292
Authors: A.R.Osborne,W.M.Clemons Jr.,T.A.Rapoport
Key ref:
A.R.Osborne et al. (2004). A large conformational change of the translocation ATPase SecA. Proc Natl Acad Sci U S A, 101, 10937-10942. PubMed id: 15256599 DOI: 10.1073/pnas.0401742101
Date:
26-May-04     Release date:   03-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P28366  (SECA_BACSU) -  Protein translocase subunit SecA from Bacillus subtilis (strain 168)
Seq:
Struc: 		 
Seq:
Struc: 		841 a.a.
772 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.7.4.2.8  - protein-secreting ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2
ATP
 + H2O
 + cellular proteinSide 1
 =
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ phosphate
 + cellular proteinSide 2
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0401742101 Proc Natl Acad Sci U S A 101:10937-10942 (2004)
PubMed id: 15256599  
 
 
A large conformational change of the translocation ATPase SecA.
A.R.Osborne, W.M.Clemons, T.A.Rapoport.
 
  ABSTRACT  
 
The ATPase SecA mediates the posttranslational translocation of a wide range of polypeptide substrates through the SecY channel in the cytoplasmic membrane of bacteria. We have determined the crystal structure of a monomeric form of Bacillus subtilis SecA at a 2.2-A resolution. A comparison with the previously determined structures of SecA reveals a nucleotide-independent, large conformational change that opens a deep groove similar to that in other proteins that interact with diverse polypeptides. We propose that the open form of SecA represents an activated state.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Structure of monomeric B. subtilis SecA. Monomeric B. subtilis SecA is presented as a ribbon diagram. NBF1 is shown in yellow, NBF2 is shown in blue, the PPXD is shown in orange, the HSD is shown in green, and the HWD is shown in cyan. ADP is shown in a ball-and-stick representation. The images were prepared by using MOLSCRIPT (40), RASTER3D (41), or SPOCK (available at http://mackerel.tamu.edu/spock). 		Figure 3.
Fig. 3. Domain movements in monomeric SecA. Ribbon diagram of monomeric B. subtilis SecA in the open conformation (a) and of a single subunit of dimeric B. subtilis SecA in the closed conformation (b). Color codes are as described for Fig. 1. The first and last helices in the PPXD are represented as cylinders to better visualize the transition between the conformations. The arrows in a indicate the movements that are required to convert the open conformation to the closed conformation. The side chains of residues 232 and 773 are shown in red in stick representation. Corresponding E. coli SecA residue numbers are given in parentheses. These residues were mutated to cysteines in E. coli SecA, and the accessibility of residue 824 to a modification reagent was used to probe the transition from the closed to the open conformation.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
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.  
20485744 H.Shruthi, P.Anand, V.Murugan, and K.Sankaran (2010).
Twin arginine translocase pathway and fast-folding lipoprotein biosynthesis in E. coli: interesting implications and applications.
  Mol Biosyst, 6, 999.  
20512970 L.L.Randall, and M.T.Henzl (2010).
Direct identification of the site of binding on the chaperone SecB for the amino terminus of the translocon motor SecA.
  Protein Sci, 19, 1173-1179.  
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.  
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.  
18978043 C.Mao, S.J.Hardy, and L.L.Randall (2009).
Maximal efficiency of coupling between ATP hydrolysis and translocation of polypeptides mediated by SecB requires two protomers of SecA.
  J Bacteriol, 191, 978-984.  
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.  
18078384 A.J.Driessen, and N.Nouwen (2008).
Protein translocation across the bacterial cytoplasmic membrane.
  Annu Rev Biochem, 77, 643-667.  
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.  
17918185 E.M.Clérico, J.L.Maki, and L.M.Gierasch (2008).
Use of synthetic signal sequences to explore the protein export machinery.
  Biopolymers, 90, 307-319.  
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
18359943 K.J.Erlandson, E.Or, A.R.Osborne, and T.A.Rapoport (2008).
Analysis of polypeptide movement in the SecY channel during SecA-mediated protein translocation.
  J Biol Chem, 283, 15709-15715.  
18923526 K.J.Erlandson, S.B.Miller, Y.Nam, A.R.Osborne, J.Zimmer, and T.A.Rapoport (2008).
A role for the two-helix finger of the SecA ATPase in protein translocation.
  Nature, 455, 984-987.  
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.  
17418789 A.R.Osborne, and T.A.Rapoport (2007).
Protein translocation is mediated by oligomers of the SecY complex with one SecY copy forming the channel.
  Cell, 129, 97.  
17511989 E.Or, and T.Rapoport (2007).
Cross-linked SecA dimers are not functional in protein translocation.
  FEBS Lett, 581, 2616-2620.  
17938627 E.Papanikou, S.Karamanou, and A.Economou (2007).
Bacterial protein secretion through the translocase nanomachine.
  Nat Rev Microbiol, 5, 839-851.  
17429388 F.Duong (2007).
Cell biology: fraternal twins.
  Nature, 446, 741-743.  
18022369 I.Gelis, A.M.Bonvin, D.Keramisanou, M.Koukaki, G.Gouridis, S.Karamanou, A.Economou, and C.G.Kalodimos (2007).
Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR.
  Cell, 131, 756-769.
PDB code: 2vda
17084862 M.Musial-Siwek, S.L.Rusch, and D.A.Kendall (2007).
Selective photoaffinity labeling identifies the signal peptide binding domain on SecA.
  J Mol Biol, 365, 637-648.  
17525736 S.Karamanou, G.Gouridis, E.Papanikou, G.Sianidis, I.Gelis, D.Keramisanou, E.Vrontou, C.G.Kalodimos, and A.Economou (2007).
Preprotein-controlled catalysis in the helicase motor of SecA.
  EMBO J, 26, 2904-2914.  
17011510 S.L.Rusch, and D.A.Kendall (2007).
Oligomeric states of the SecA and SecYEG core components of the bacterial Sec translocon.
  Biochim Biophys Acta, 1768, 5.  
17676771 S.L.Rusch, and D.A.Kendall (2007).
Interactions that drive Sec-dependent bacterial protein transport.
  Biochemistry, 46, 9665-9673.  
18046402 T.A.Rapoport (2007).
Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes.
  Nature, 450, 663-669.  
17419072 Y.Chen, P.C.Tai, and S.F.Sui (2007).
The active ring-like structure of SecA revealed by electron crystallography: conformational change upon interaction with SecB.
  J Struct Biol, 159, 149-153.  
16731972 C.N.Patel, V.F.Smith, and L.L.Randall (2006).
Characterization of three areas of interactions stabilizing complexes between SecA and SecB, two proteins involved in protein export.
  Protein Sci, 15, 1379-1386.  
16783375 D.Keramisanou, N.Biris, I.Gelis, G.Sianidis, S.Karamanou, A.Economou, and C.G.Kalodimos (2006).
Disorder-order folding transitions underlie catalysis in the helicase motor of SecA.
  Nat Struct Mol Biol, 13, 594-602.  
16962134 J.M.Crane, Y.Suo, A.A.Lilly, C.Mao, W.L.Hubbell, and L.L.Randall (2006).
Sites of interaction of a precursor polypeptide on the export chaperone SecB mapped by site-directed spin labeling.
  J Mol Biol, 363, 63-74.  
16352850 L.B.Jilaveanu, and D.Oliver (2006).
SecA dimer cross-linked at its subunit interface is functional for protein translocation.
  J Bacteriol, 188, 335-338.  
  16946477 M.N.Vassylyeva, H.Mori, T.Tsukazaki, S.Yokoyama, T.H.Tahirov, K.Ito, and D.G.Vassylyev (2006).
Cloning, expression, purification, crystallization and initial crystallographic analysis of the preprotein translocation ATPase SecA from Thermus thermophilus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 909-912.  
  16754988 W.Meining, J.Scheuring, M.Fischer, and S.Weinkauf (2006).
Cloning, purification, crystallization and preliminary crystallographic analysis of SecA from Enterococcus faecalis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 583-585.  
16212506 A.R.Osborne, T.A.Rapoport, and B.van den Berg (2005).
Protein translocation by the Sec61/SecY channel.
  Annu Rev Cell Dev Biol, 21, 529-550.  
15713839 H.Nakatogawa, A.Murakami, H.Mori, and K.Ito (2005).
SecM facilitates translocase function of SecA by localizing its biosynthesis.
  Genes Dev, 19, 436-444.  
16153172 J.Luirink, G.von Heijne, E.Houben, and J.W.de Gier (2005).
Biogenesis of inner membrane proteins in Escherichia coli.
  Annu Rev Microbiol, 59, 329-355.  
16194224 J.Zhou, and Z.Xu (2005).
The structural view of bacterial translocation-specific chaperone SecB: implications for function.
  Mol Microbiol, 58, 349-357.  
15851514 K.S.Cannon, E.Or, W.M.Clemons, Y.Shibata, and T.A.Rapoport (2005).
Disulfide bridge formation between SecY and a translocating polypeptide localizes the translocation pore to the center of SecY.
  J Cell Biol, 169, 219-225.  
15897468 L.B.Jilaveanu, C.R.Zito, and D.Oliver (2005).
Dimeric SecA is essential for protein translocation.
  Proc Natl Acad Sci U S A, 102, 7511-7516.  
16229488 M.Musial-Siwek, S.L.Rusch, and D.A.Kendall (2005).
Probing the affinity of SecA for signal peptide in different environments.
  Biochemistry, 44, 13987-13996.  
15502345 K.Yamane, K.Bunai, and H.Kakeshita (2004).
Protein traffic for secretion and related machinery of Bacillus subtilis.
  Biosci Biotechnol Biochem, 68, 2007-2023.  
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.

 

spacer
spacer