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Hydrolase PDB id
1lv7
Jmol
Contents
Protein chain
251 a.a. *
Ligands
SO4 ×5
Waters ×366
* Residue conservation analysis
PDB id:
1lv7
Name: Hydrolase
Title: Crystal structure of the aaa domain of ftsh
Structure: Ftsh. Chain: a. Fragment: aaa domain. Synonym: cell division protein ftsh. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: ftsh. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
1.50Å     R-factor:   0.155     R-free:   0.178
Authors: S.Krzywda,A.M.Brzozowski,C.Verma,K.Karata,T.Ogura,A.J.Wilkin
Key ref:
S.Krzywda et al. (2002). The crystal structure of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli at 1.5 A resolution. Structure, 10, 1073-1083. PubMed id: 12176385 DOI: 10.1016/S0969-2126(02)00806-7
Date:
26-May-02     Release date:   09-Oct-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AAI3  (FTSH_ECOLI) -  ATP-dependent zinc metalloprotease FtsH
Seq:
Struc: 		 
Seq:
Struc: 		644 a.a.
251 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 
  Biological process     protein catabolic process   1 term 
  Biochemical function     nucleotide binding     4 terms  

 

 
DOI no: 10.1016/S0969-2126(02)00806-7 Structure 10:1073-1083 (2002)
PubMed id: 12176385  
 
 
The crystal structure of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli at 1.5 A resolution.
S.Krzywda, A.M.Brzozowski, C.Verma, K.Karata, T.Ogura, A.J.Wilkinson.
 
  ABSTRACT  
 
Eubacteria and eukaryotic cellular organelles have membrane-bound ATP-dependent proteases, which degrade misassembled membrane protein complexes and play a vital role in membrane quality control. The bacterial protease FtsH also degrades an interesting subset of cytoplasmic regulatory proteins, including sigma(32), LpxC, and lambda CII. The crystal structure of the ATPase module of FtsH has been solved, revealing an alpha/beta nucleotide binding domain connected to a four-helix bundle, similar to the AAA modules of proteins involved in DNA replication and membrane fusion. A sulfate anion in the ATP binding pocket mimics the beta-phosphate group of an adenine nucleotide. A hexamer form of FtsH has been modeled, providing insights into possible modes of nucleotide binding and intersubunit catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19596908 W.B.Inwood, J.A.Hall, K.S.Kim, L.Demirkhanyan, D.Wemmer, H.Zgurskaya, and S.Kustu (2009).
Epistatic effects of the protease/chaperone HflB on some damaged forms of the Escherichia coli ammonium channel AmtB.
  Genetics, 183, 1327-1340.  
18394159 J.C.Zweers, I.Barák, D.Becher, A.J.Driessen, M.Hecker, V.P.Kontinen, M.J.Saller, L.Vavrová, and J.M.van Dijl (2008).
Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes.
  Microb Cell Fact, 7, 10.  
18326037 N.Joly, P.C.Burrows, and M.Buck (2008).
An intramolecular route for coupling ATPase activity in AAA+ proteins for transcription activation.
  J Biol Chem, 283, 13725-13735.  
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
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.  
17822404 A.Karnataki, A.E.Derocher, I.Coppens, J.E.Feagin, and M.Parsons (2007).
A membrane protease is targeted to the relict plastid of toxoplasma via an internal signal sequence.
  Traffic, 8, 1543-1553.  
17427253 A.Winter, O.Kämäräinen, and A.Hofmann (2007).
Molecular modeling of prohibitin domains.
  Proteins, 68, 353-362.  
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.  
17883390 N.Joly, M.Rappas, S.R.Wigneshweraraj, X.Zhang, and M.Buck (2007).
Coupling nucleotide hydrolysis to transcription activation performance in a bacterial enhancer binding protein.
  Mol Microbiol, 66, 583-595.  
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
16286465 J.Komenda, M.Barker, S.Kuviková, R.de Vries, C.W.Mullineaux, M.Tichy, and P.J.Nixon (2006).
The FtsH protease slr0228 is important for quality control of photosystem II in the thylakoid membrane of Synechocystis sp. PCC 6803.
  J Biol Chem, 281, 1145-1151.  
16689629 J.P.Erzberger, and J.M.Berger (2006).
Evolutionary relationships and structural mechanisms of AAA+ proteins.
  Annu Rev Biophys Biomol Struct, 35, 93.  
17181860 M.García-Lorenzo, A.Sjödin, S.Jansson, and C.Funk (2006).
Protease gene families in Populus and Arabidopsis.
  BMC Plant Biol, 6, 30.  
16973614 N.Joly, J.Schumacher, and M.Buck (2006).
Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA+ transcriptional activator.
  J Biol Chem, 281, 34997-35007.  
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
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.  
16669775 W.Sakamoto (2006).
Protein degradation machineries in plastids.
  Annu Rev Plant Biol, 57, 599-621.  
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.  
16216872 Q.Wang, C.Song, L.Irizarry, R.Dai, X.Zhang, and C.C.Li (2005).
Multifunctional roles of the conserved Arg residues in the second region of homology of p97/valosin-containing protein.
  J Biol Chem, 280, 40515-40523.  
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.  
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.  
15803409 W.Sakamoto, E.Miura, Y.Kaji, T.Okuno, M.Nishizono, and T.Ogura (2004).
Allelic characterization of the leaf-variegated mutation var2 identifies the conserved amino acid residues of FtsH that are important for ATP hydrolysis and proteolysis.
  Plant Mol Biol, 56, 705-716.  
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
12950913 R.Hengge, and B.Bukau (2003).
Proteolysis in prokaryotes: protein quality control and regulatory principles.
  Mol Microbiol, 49, 1451-1462.  
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 codes are shown on the right.