spacer
spacer

PDBsum entry 1ixz

Go to PDB code: 
protein ligands metals links
Hydrolase PDB id
1ixz
Jmol
Contents
Protein chain
238 a.a. *
Ligands
SO4 ×3
Metals
_HG ×2
Waters ×150
* Residue conservation analysis
PDB id:
1ixz
Name: Hydrolase
Title: Crystal structure of the ftsh atpase domain from thermus thermophilus
Structure: Atp-dependent metalloprotease ftsh. Chain: a. Fragment: f1. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Gene: ftsh. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.20Å     R-factor:   0.196     R-free:   0.238
Authors: H.Niwa,D.Tsuchiya,H.Makyio,M.Yoshida,K.Morikawa
Key ref:
H.Niwa et al. (2002). Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8. Structure, 10, 1415-1423. PubMed id: 12377127 DOI: 10.1016/S0969-2126(02)00855-9
Date:
10-Jul-02     Release date:   06-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SI82  (FTSH_THET8) -  ATP-dependent zinc metalloprotease FtsH
Seq:
Struc:
 
Seq:
Struc:
624 a.a.
238 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biochemical function     nucleotide binding     4 terms  

 

 
DOI no: 10.1016/S0969-2126(02)00855-9 Structure 10:1415-1423 (2002)
PubMed id: 12377127  
 
 
Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8.
H.Niwa, D.Tsuchiya, H.Makyio, M.Yoshida, K.Morikawa.
 
  ABSTRACT  
 
FtsH is a cytoplasmic membrane-integrated, ATP-dependent metalloprotease, which processively degrades both cytoplasmic and membrane proteins in concert with unfolding. The FtsH protein is divided into the N-terminal transmembrane region and the larger C-terminal cytoplasmic region, which consists of an ATPase domain and a protease domain. We have determined the crystal structures of the Thermus thermophilus FtsH ATPase domain in the nucleotide-free and AMP-PNP- and ADP-bound states, in addition to the domain with the extra preceding segment. Combined with the mapping of the putative substrate binding region, these structures suggest that FtsH internally forms a hexameric ring structure, in which ATP binding could cause a conformational change to facilitate transport of substrates into the protease domain through the central pore.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Hexameric Ring Model of the FtsH ATPase Domain(A) The figures are viewed from the transmembrane side (left) and the protease domain side (right). From the extra segment position of the FtsH-F2 crystal structure, we found that the transmembrane helices are located on the N-terminal side of the hexagonal plate. The model possesses an outer diameter of approximately 120 , with a central pore of 13 in diameter. Note the gap between subunits, which becomes narrow in comparison with that in the crystal packing arrangement, as shown in Figure 1D. The rotation angle between subdomains in the model differs by 34 from that in the crystal. Although every subunit is represented with the same conformation in this model, the mode of the ATPase cycle, either sequential or synchronized, cannot be clarified.(B) Representation of the arginine finger in the model viewed from the transmembrane side. Arg313 is located at a position capable of interacting with the g-phosphate of AMP-PNP bound to a neighboring subunit. The SRH motif, highlighted in pink, is located on the contact surface between subunits. The a7 helix and the following loop in front of Arg313 are eliminated.(C) SRH motif in the model, viewed from the protease domain side. The motif from the AMP-PNP form is superimposed onto that from the ADP form. The Ca atom of Asn302 is colored red.(D) Mapping of the putative substrate binding regions (brown). Note that the MFVG sequence (green) faces the central pore. A closed line indicates a monomer structure, corresponding to the highlighted one in (A).(E) Electrostatic potential surfaces of the model, calculated by the program GRASP [52]. Red and blue represent regions of negative and positive potential, respectively.
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 1415-1423) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21214651 R.A.Rodrigues, M.C.Silva-Filho, and K.Cline (2011).
FtsH2 and FtsH5: two homologous subunits use different integration mechanisms leading to the same thylakoid multimeric complex.
  Plant J, 65, 600-609.  
21269440 Y.Peng, Y.Luo, T.Yu, X.Xu, K.Fan, Y.Zhao, and K.Yang (2011).
A Blue Native-PAGE analysis of membrane protein complexes in Clostridium thermocellum.
  BMC Microbiol, 11, 22.  
20564558 T.Kinouchi, and N.Fujii (2010).
Structural consideration of mammalian D-aspartyl endopeptidase.
  Chem Biodivers, 7, 1403-1407.  
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.  
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
19617353 M.Khatoon, K.Inagawa, P.Pospísil, A.Yamashita, M.Yoshioka, B.Lundin, J.Horie, N.Morita, A.Jajoo, Y.Yamamoto, and Y.Yamamoto (2009).
Quality control of photosystem II: Thylakoid unstacking is necessary to avoid further damage to the D1 protein and to facilitate D1 degradation under light stress in spinach thylakoids.
  J Biol Chem, 284, 25343-25352.  
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
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.  
18937045 Y.Yamamoto, R.Aminaka, M.Yoshioka, M.Khatoon, K.Komayama, D.Takenaka, A.Yamashita, N.Nijo, K.Inagawa, N.Morita, T.Sasaki, and Y.Yamamoto (2008).
Quality control of photosystem II: impact of light and heat stresses.
  Photosynth Res, 98, 589-608.  
18023171 P.A.Tucker, and L.Sallai (2007).
The AAA+ superfamily--a myriad of motions.
  Curr Opin Struct Biol, 17, 641-652.  
17292836 Y.Nakamura, K.Nakano, T.Umehara, M.Kimura, Y.Hayashizaki, A.Tanaka, M.Horikoshi, B.Padmanabhan, and S.Yokoyama (2007).
Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome.
  Structure, 15, 179-189.
PDB codes: 2dvw 2dwz
16689629 J.P.Erzberger, and J.M.Berger (2006).
Evolutionary relationships and structural mechanisms of AAA+ proteins.
  Annu Rev Biophys Biomol Struct, 35, 93.  
16430918 M.Rappas, J.Schumacher, H.Niwa, M.Buck, and X.Zhang (2006).
Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF.
  J Mol Biol, 357, 481-492.
PDB codes: 2c96 2c98 2c99 2c9c
16762831 R.Suno, H.Niwa, D.Tsuchiya, X.Zhang, M.Yoshida, and K.Morikawa (2006).
Structure of the whole cytosolic region of ATP-dependent protease FtsH.
  Mol Cell, 22, 575-585.
PDB codes: 2dhr 2di4 4eiw
16573693 S.Chiba, K.Ito, and Y.Akiyama (2006).
The Escherichia coli plasma membrane contains two PHB (prohibitin homology) domain protein complexes of opposite orientations.
  Mol Microbiol, 60, 448-457.  
16483314 T.Okuno, K.Yamanaka, and T.Ogura (2006).
An AAA protease FtsH can initiate proteolysis from internal sites of a model substrate, apo-flavodoxin.
  Genes Cells, 11, 261-268.  
16877706 T.V.Rotanova, I.Botos, E.E.Melnikov, F.Rasulova, A.Gustchina, M.R.Maurizi, and A.Wlodawer (2006).
Slicing a protease: structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domains.
  Protein Sci, 15, 1815-1828.  
16193069 A.Scott, H.Y.Chung, M.Gonciarz-Swiatek, G.C.Hill, F.G.Whitby, J.Gaspar, J.M.Holton, R.Viswanathan, S.Ghaffarian, C.P.Hill, and W.I.Sundquist (2005).
Structural and mechanistic studies of VPS4 proteins.
  EMBO J, 24, 3658-3669.
PDB code: 1xwi
16247555 A.Urantowka, C.Knorpp, T.Olczak, M.Kolodziejczak, and H.Janska (2005).
Plant mitochondria contain at least two i-AAA-like complexes.
  Plant Mol Biol, 59, 239-252.  
15910274 K.Ito, and Y.Akiyama (2005).
Cellular functions, mechanism of action, and regulation of FtsH protease.
  Annu Rev Microbiol, 59, 211-231.  
15181012 A.Y.Lee, C.H.Hsu, and S.H.Wu (2004).
Functional domains of Brevibacillus thermoruber lon protease for oligomerization and DNA binding: role of N-terminal and sensor and substrate discrimination domains.
  J Biol Chem, 279, 34903-34912.  
15208691 C.Schlieker, J.Weibezahn, H.Patzelt, P.Tessarz, C.Strub, K.Zeth, A.Erbse, J.Schneider-Mergener, J.W.Chin, P.G.Schultz, B.Bukau, and A.Mogk (2004).
Substrate recognition by the AAA+ chaperone ClpB.
  Nat Struct Mol Biol, 11, 607-615.  
14996218 F.Yu, S.Park, and S.R.Rodermel (2004).
The Arabidopsis FtsH metalloprotease gene family: interchangeability of subunits in chloroplast oligomeric complexes.
  Plant J, 37, 864-876.  
15201901 G.D.Bowman, M.O'Donnell, and J.Kuriyan (2004).
Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex.
  Nature, 429, 724-730.
PDB code: 1sxj
14665623 I.Botos, E.E.Melnikov, S.Cherry, J.E.Tropea, A.G.Khalatova, F.Rasulova, Z.Dauter, M.R.Maurizi, T.V.Rotanova, A.Wlodawer, and A.Gustchina (2004).
The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site.
  J Biol Chem, 279, 8140-8148.
PDB codes: 1rr9 1rre
14988733 I.Dreveny, H.Kondo, K.Uchiyama, A.Shaw, X.Zhang, and P.S.Freemont (2004).
Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47.
  EMBO J, 23, 1030-1039.
PDB code: 1s3s
14757246 M.Kotschwar, S.Diermeier, and W.Schumann (2004).
The yjoB gene of Bacillus subtilis encodes a protein that is a novel member of the AAA family.
  FEMS Microbiol Lett, 230, 241-249.  
14962378 M.R.Maurizi, and D.Xia (2004).
Protein binding and disruption by Clp/Hsp100 chaperones.
  Structure, 12, 175-183.  
14688254 M.Zhang, and P.Coffino (2004).
Repeat sequence of Epstein-Barr virus-encoded nuclear antigen 1 protein interrupts proteasome substrate processing.
  J Biol Chem, 279, 8635-8641.  
12667449 C.Herman, S.Prakash, C.Z.Lu, A.Matouschek, and C.A.Gross (2003).
Lack of a robust unfoldase activity confers a unique level of substrate specificity to the universal AAA protease FtsH.
  Mol Cell, 11, 659-669.  
14514695 D.Y.Kim, and K.K.Kim (2003).
Crystal structure of ClpX molecular chaperone from Helicobacter pylori.
  J Biol Chem, 278, 50664-50670.
PDB code: 1um8
14570582 S.Gottesman (2003).
Proteolysis in bacterial regulatory circuits.
  Annu Rev Cell Dev Biol, 19, 565-587.  
14514680 T.Yamada-Inagawa, T.Okuno, K.Karata, K.Yamanaka, and T.Ogura (2003).
Conserved pore residues in the AAA protease FtsH are important for proteolysis and its coupling to ATP hydrolysis.
  J Biol Chem, 278, 50182-50187.  
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.