spacer
spacer

PDBsum entry 4eiw
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
4eiw

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
(+ 0 more) 458 a.a.
Ligands
ADP ×6
PDB id:
4eiw
Name: Hydrolase
Title: Whole cytosolic region of atp-dependent metalloprotease ftsh (g399l)
Structure: Atp-dependent zinc metalloprotease ftsh. Chain: a, b, c, d, e, f. Fragment: soluble region, unp residues 126-624. Engineered: yes. Mutation: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: ftsh, ttha1492. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.90Å     R-factor:   0.300     R-free:   0.312
Authors: R.Suno,H.Niwa,D.Tsuchiya,M.Yoshida,K.Morikawa
Key ref:
R.Suno et al. (2006). Structure of the whole cytosolic region of ATP-dependent protease FtsH. Mol Cell, 22, 575-585. PubMed id: 16762831 DOI: 10.1016/j.molcel.2006.04.020
Date:
06-Apr-12     Release date:   06-Jun-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5SI82  (FTSH_THET8) -  ATP-dependent zinc metalloprotease FtsH from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		 
Seq:
Struc: 		624 a.a.
458 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.3.4.24.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.molcel.2006.04.020 Mol Cell 22:575-585 (2006)
PubMed id: 16762831  
 
 
Structure of the whole cytosolic region of ATP-dependent protease FtsH.
R.Suno, H.Niwa, D.Tsuchiya, X.Zhang, M.Yoshida, K.Morikawa.
 
  ABSTRACT  
 
An ATP-dependent protease, FtsH, digests misassembled membrane proteins in order to maintain membrane integrity and digests short-lived soluble proteins in order to control their cellular regulation. This enzyme has an N-terminal transmembrane segment and a C-terminal cytosolic region consisting of an AAA+ ATPase domain and a protease domain. Here we present two crystal structures: the protease domain and the whole cytosolic region. The cytosolic region fully retains an ATP-dependent protease activity and adopts a three-fold-symmetric hexameric structure. The protease domains displayed a six-fold symmetry, while the AAA+ domains, each containing ADP, alternate two orientations relative to the protease domain, making "open" and "closed" interdomain contacts. Apparently, ATPase is active only in the closed form, and protease operates in the open form. The protease catalytic sites are accessible only through a tunnel following from the AAA+ domain of the adjacent subunit, raising a possibility of translocation of polypeptide substrate to the protease sites through this tunnel.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Catalytic Environments in sFtsH 		Figure 6.
Figure 6. The ATPase Cycle and Putative Polypeptide Translocation Pathway
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 22, 575-585) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22307055 L.F.Chang, S.Chen, C.C.Liu, X.Pan, J.Jiang, X.C.Bai, X.Xie, H.W.Wang, and S.F.Sui (2012).
Structural characterization of full-length NSF and 20S particles.
  Nat Struct Mol Biol, 19, 268-275.  
22398446 T.Kon, T.Oyama, R.Shimo-Kon, K.Imamula, T.Shima, K.Sutoh, and G.Kurisu (2012).
The 2.8 Å crystal structure of the dynein motor domain.
  Nature, 484, 345-350.
PDB codes: 3vkg 3vkh
21282052 A.Y.Lyubimov, M.Strycharska, and J.M.Berger (2011).
The nuts and bolts of ring-translocase structure and mechanism.
  Curr Opin Struct Biol, 21, 240-248.  
22020261 E.Gur, D.Biran, and E.Z.Ron (2011).
Regulated proteolysis in Gram-negative bacteria--how and when?
  Nat Rev Microbiol, 9, 839-848.  
19887446 C.Zhao, E.A.Matveeva, Q.Ren, and S.W.Whiteheart (2010).
Dissecting the N-ethylmaleimide-sensitive factor: required elements of the N and D1 domains.
  J Biol Chem, 285, 761-772.  
20208537 D.Di Bella, F.Lazzaro, A.Brusco, M.Plumari, G.Battaglia, A.Pastore, A.Finardi, C.Cagnoli, F.Tempia, M.Frontali, L.Veneziano, T.Sacco, E.Boda, A.Brussino, F.Bonn, B.Castellotti, S.Baratta, C.Mariotti, C.Gellera, V.Fracasso, S.Magri, T.Langer, P.Plevani, S.Di Donato, M.Muzi-Falconi, and F.Taroni (2010).
Mutations in the mitochondrial protease gene AFG3L2 cause dominant hereditary ataxia SCA28.
  Nat Genet, 42, 313-321.  
20130684 M.Esaki, and T.Ogura (2010).
ATP-bound form of the D1 AAA domain inhibits an essential function of Cdc48p/p97.
  Biochem Cell Biol, 88, 109-117.  
20834233 S.S.Cha, Y.J.An, C.R.Lee, H.S.Lee, Y.G.Kim, S.J.Kim, K.K.Kwon, G.M.De Donatis, J.H.Lee, M.R.Maurizi, and S.G.Kang (2010).
Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber.
  EMBO J, 29, 3520-3530.
PDB code: 3k1j
20666930 X.Liu, F.Yu, and S.Rodermel (2010).
Arabidopsis chloroplast FtsH, var2 and suppressors of var2 leaf variegation: a review.
  J Integr Plant Biol, 52, 750-761.  
19450729 A.Karnataki, A.E.DeRocher, J.E.Feagin, and M.Parsons (2009).
Sequential processing of the Toxoplasma apicoplast membrane protein FtsH1 in topologically distinct domains during intracellular trafficking.
  Mol Biochem Parasitol, 166, 126-133.  
19332814 A.T.Le, and W.Schumann (2009).
The Spo0E phosphatase of Bacillus subtilis is a substrate of the FtsH metalloprotease.
  Microbiology, 155, 1122-1132.  
19955424 C.Bieniossek, B.Niederhauser, and U.M.Baumann (2009).
The crystal structure of apo-FtsH reveals domain movements necessary for substrate unfolding and translocation.
  Proc Natl Acad Sci U S A, 106, 21579-21584.
PDB code: 3kds
19362814 F.Striebel, W.Kress, and E.Weber-Ban (2009).
Controlled destruction: AAA+ ATPases in protein degradation from bacteria to eukaryotes.
  Curr Opin Struct Biol, 19, 209-217.  
19361443 G.Effantin, R.Rosenzweig, M.H.Glickman, and A.C.Steven (2009).
Electron microscopic evidence in support of alpha-solenoid models of proteasomal subunits Rpn1 and Rpn2.
  J Mol Biol, 386, 1204-1211.  
19748354 S.Augustin, F.Gerdes, S.Lee, F.T.Tsai, T.Langer, and T.Tatsuta (2009).
An intersubunit signaling network coordinates ATP hydrolysis by m-AAA proteases.
  Mol Cell, 35, 574-585.  
19841671 T.Karlberg, S.van den Berg, M.Hammarström, J.Sagemark, I.Johansson, L.Holmberg-Schiavone, and H.Schüler (2009).
Crystal structure of the ATPase domain of the human AAA+ protein paraplegin/SPG7.
  PLoS One, 4, e6975.
PDB code: 2qz4
18462676 J.M.Davies, A.T.Brunger, and W.I.Weis (2008).
Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change.
  Structure, 16, 715-726.
PDB codes: 3cf0 3cf1 3cf2 3cf3
18466635 J.Snider, G.Thibault, and W.A.Houry (2008).
The AAA+ superfamily of functionally diverse proteins.
  Genome Biol, 9, 216.  
18929572 M.D.Gonciarz, F.G.Whitby, D.M.Eckert, C.Kieffer, A.Heroux, W.I.Sundquist, and C.P.Hill (2008).
Biochemical and structural studies of yeast Vps4 oligomerization.
  J Mol Biol, 384, 878-895.
PDB codes: 3eie 3eih
18647240 N.D.Thomsen, and J.M.Berger (2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
  Mol Microbiol, 69, 1071-1090.  
18421140 S.H.Kim, G.B.Kang, H.E.Song, S.J.Park, M.H.Bea, and S.H.Eom (2008).
Structural studies on Helicobacter pyloriATP-dependent protease, FtsH.
  J Synchrotron Radiat, 15, 208-210.
PDB codes: 2r62 2r65
18670904 S.I.Allakhverdiev, and N.Murata (2008).
Salt stress inhibits photosystems II and I in cyanobacteria.
  Photosynth Res, 98, 529-539.  
19011636 T.Masaike, F.Koyama-Horibe, K.Oiwa, M.Yoshida, and T.Nishizaka (2008).
Cooperative three-step motions in catalytic subunits of F(1)-ATPase correlate with 80 degrees and 40 degrees substep rotations.
  Nat Struct Mol Biol, 15, 1326-1333.  
17242399 J.Schumacher, N.Joly, M.Rappas, D.Bradley, S.R.Wigneshweraraj, X.Zhang, and M.Buck (2007).
Sensor I threonine of the AAA+ ATPase transcriptional activator PspF is involved in coupling nucleotide triphosphate hydrolysis to the restructuring of sigma 54-RNA polymerase.
  J Biol Chem, 282, 9825-9833.  
17261594 M.Graef, G.Seewald, and T.Langer (2007).
Substrate recognition by AAA+ ATPases: distinct substrate binding modes in ATP-dependent protease Yme1 of the mitochondrial intermembrane space.
  Mol Cell Biol, 27, 2476-2485.  
17101804 M.Koppen, M.D.Metodiev, G.Casari, E.I.Rugarli, and T.Langer (2007).
Variable and tissue-specific subunit composition of mitochondrial m-AAA protease complexes linked to hereditary spastic paraplegia.
  Mol Cell Biol, 27, 758-767.  
18073113 M.Kuratani, Y.Yoshikawa, Y.Bessho, K.Higashijima, T.Ishii, R.Shibata, S.Takahashi, K.Yutani, and S.Yokoyama (2007).
Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine.
  Structure, 15, 1642-1653.
PDB codes: 2e21 2e89
17157497 M.Rappas, D.Bose, and X.Zhang (2007).
Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription.
  Curr Opin Struct Biol, 17, 110-116.  
18023171 P.A.Tucker, and L.Sallai (2007).
The AAA+ superfamily--a myriad of motions.
  Curr Opin Struct Biol, 17, 641-652.  
17245427 T.Tatsuta, S.Augustin, M.Nolden, B.Friedrichs, and T.Langer (2007).
m-AAA protease-driven membrane dislocation allows intramembrane cleavage by rhomboid in mitochondria.
  EMBO J, 26, 325-335.  
17112720 P.R.Mittl, and M.G.Grütter (2006).
Opportunities for structure-based design of protease-directed drugs.
  Curr Opin Struct Biol, 16, 769-775.  
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