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PDBsum entry 1w5a

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protein ligands metals Protein-protein interface(s) links
Cell division PDB id
1w5a
Jmol
Contents
Protein chains
334 a.a. *
Ligands
GTP ×2
Metals
_MG
Waters ×247
* Residue conservation analysis
PDB id:
1w5a
Name: Cell division
Title: Ftsz dimer, mggtp soak (m. Jannaschii)
Structure: Cell division protein ftsz homolog 1. Chain: a, b. Synonym: ftsz. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Atcc: 43067. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.4Å     R-factor:   0.218     R-free:   0.264
Authors: M.A.Oliva,S.C.Cordell,J.Lowe
Key ref:
M.A.Oliva et al. (2004). Structural insights into FtsZ protofilament formation. Nat Struct Mol Biol, 11, 1243-1250. PubMed id: 15558053 DOI: 10.1038/nsmb855
Date:
06-Aug-04     Release date:   01-Dec-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q57816  (FTSZ1_METJA) -  Cell division protein FtsZ 1
Seq:
Struc:
364 a.a.
334 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   3 terms 
  Biological process     cell cycle   6 terms 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1038/nsmb855 Nat Struct Mol Biol 11:1243-1250 (2004)
PubMed id: 15558053  
 
 
Structural insights into FtsZ protofilament formation.
M.A.Oliva, S.C.Cordell, J.Löwe.
 
  ABSTRACT  
 
The prokaryotic tubulin homolog FtsZ polymerizes into a ring structure essential for bacterial cell division. We have used refolded FtsZ to crystallize a tubulin-like protofilament. The N- and C-terminal domains of two consecutive subunits in the filament assemble to form the GTPase site, with the C-terminal domain providing water-polarizing residues. A domain-swapped structure of FtsZ and biochemical data on purified N- and C-terminal domains show that they are independent. This leads to a model of how FtsZ and tubulin polymerization evolved by fusing two domains. In polymerized tubulin, the nucleotide-binding pocket is occluded, which leads to nucleotide exchange being the rate-limiting step and to dynamic instability. In our FtsZ filament structure the nucleotide is exchangeable, explaining why, in this filament, nucleotide hydrolysis is the rate-limiting step during FtsZ polymerization. Furthermore, crystal structures of FtsZ in different nucleotide states reveal notably few differences.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Detailed view of the intersubunit active sites in MjFtsZ and tubulin. (a) FtsZ dimer. The GTPase domain of the lower subunit is complemented by two aspartates (Asp235 and Asp238) that polarize the attacking water molecule (Wat105). Apart from these residues, which belong to loop T7, S9 and helix H10 of the C-terminal domain of FtsZ are involved in the protofilament contact. (b) / tubulin (PDB entry 1JFF) with -tubulin on top (not the tubulin solution dimer, but the catalytically active contact formed in protofilaments). The general arrangement in the active site is very similar to that of FtsZ with T7, S9 and H10 of the C-terminal (intermediate) domain making the protofilament contact. Very little space would be left for a -phosphate, and the polarizing acidic residue, Glu254, is not in the right position to polarize the attacking water molecule. The tubulin structure was solved at low resolution and exact side chain positions may not be known for all residues.
Figure 5.
Figure 5. A lack of conformational changes in different FtsZ structures. (a) M. jannaschii FtsZ with bound GMPCPP at a resolution of 2.5 Å. GDP-containing crystals were soaked with magnesium and GMCPP in a special buffer to replace the bound nucleotide. The -phosphate occupies the previously identified binding pocket^6, making hydrogen bonding contacts to loop T3. (b) Superposition of M. jannaschii FtsZ active sites: minimal changes are observed between the structures of monomers containing nucleotides and the refolded, empty monomer in completely different space groups and packing arrangements. Stereo drawing.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 1243-1250) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22806143 M.V.Brown, F.M.Lauro, M.Z.Demaere, L.Muir, D.Wilkins, T.Thomas, M.J.Riddle, J.A.Fuhrman, C.Andrews-Pfannkoch, J.M.Hoffman, J.B.McQuaid, A.Allen, S.R.Rintoul, and R.Cavicchioli (2012).
Global biogeography of SAR11 marine bacteria.
  Mol Syst Biol, 8, 595.  
21413908 D.Awasthi, K.Kumar, and I.Ojima (2011).
Therapeutic potential of FtsZ inhibition: a patent perspective.
  Expert Opin Ther Pat, 21, 657-679.  
  21276094 D.W.Adams, L.J.Wu, L.G.Czaplewski, and J.Errington (2011).
Multiple effects of benzamide antibiotics on FtsZ function.
  Mol Microbiol, 80, 68-84.  
20974911 C.H.Aylett, Q.Wang, K.A.Michie, L.A.Amos, and J.Löwe (2010).
Filament structure of bacterial tubulin homologue TubZ.
  Proc Natl Acad Sci U S A, 107, 19766-19771.
PDB codes: 2xka 2xkb
21059902 E.Nogales (2010).
When cytoskeletal worlds collide.
  Proc Natl Acad Sci U S A, 107, 19609-19610.  
20559630 J.Hritz, T.Läppchen, and C.Oostenbrink (2010).
Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ.
  Eur Biophys J, 39, 1573-1580.  
20598544 J.Mingorance, G.Rivas, M.Vélez, P.Gómez-Puertas, and M.Vicente (2010).
Strong FtsZ is with the force: mechanisms to constrict bacteria.
  Trends Microbiol, 18, 348-356.  
20534443 L.Ni, W.Xu, M.Kumaraswami, and M.A.Schumacher (2010).
Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition.
  Proc Natl Acad Sci U S A, 107, 11763-11768.
PDB codes: 3m89 3m8e 3m8f 3m8k 3m9a
21047262 M.T.Cabeen, and C.Jacobs-Wagner (2010).
The bacterial cytoskeleton.
  Annu Rev Genet, 44, 365-392.  
20497333 S.Alexeeva, T.W.Gadella, J.Verheul, G.S.Verhoeven, and T.den Blaauwen (2010).
Direct interactions of early and late assembling division proteins in Escherichia coli cells resolved by FRET.
  Mol Microbiol, 77, 384-398.  
20022957 S.Sugimoto, K.Yamanaka, S.Nishikori, A.Miyagi, T.Ando, and T.Ogura (2010).
AAA+ chaperone ClpX regulates dynamics of prokaryotic cytoskeletal protein FtsZ.
  J Biol Chem, 285, 6648-6657.  
19383143 A.Raymond, S.Lovell, D.Lorimer, J.Walchli, M.Mixon, E.Wallace, K.Thompkins, K.Archer, A.Burgin, and L.Stewart (2009).
Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer.
  BMC Biotechnol, 9, 37.
PDB codes: 2rhh 2rhj 2rhl 2rho
19740076 D.Dasgupta (2009).
Novel compound with potential of an antibacterial drug targets FtsZ protein.
  Biochem J, 423, e1-e3.  
19680248 D.W.Adams, and J.Errington (2009).
Bacterial cell division: assembly, maintenance and disassembly of the Z ring.
  Nat Rev Microbiol, 7, 642-653.  
18768164 J.Löwe, and L.A.Amos (2009).
Evolution of cytomotive filaments: the cytoskeleton from prokaryotes to eukaryotes.
  Int J Biochem Cell Biol, 41, 323-329.  
19262024 M.Fujihara, K.Maeda, E.Sasamori, M.Matsushita, and R.Harasawa (2009).
Effects of chelating reagents on colonial appearance of Paenibacillus alvei isolated from canine oral cavity.
  J Vet Med Sci, 71, 147-153.  
19466751 P.L.Graumann (2009).
Dynamics of bacterial cytoskeletal elements.
  Cell Motil Cytoskeleton, 66, 909-914.  
19565362 R.H.Wade (2009).
On and around microtubules: an overview.
  Mol Biotechnol, 43, 177-191.  
18284588 A.A.Handler, J.E.Lim, and R.Losick (2008).
Peptide inhibitor of cytokinesis during sporulation in Bacillus subtilis.
  Mol Microbiol, 68, 588-599.  
18502809 E.R.Miraldi, P.J.Thomas, and L.Romberg (2008).
Allosteric models for cooperative polymerization of linear polymers.
  Biophys J, 95, 2470-2486.  
18604268 I.V.Surovtsev, J.J.Morgan, and P.A.Lindahl (2008).
Kinetic modeling of the assembly, dynamic steady state, and contraction of the FtsZ ring in prokaryotic cytokinesis.
  PLoS Comput Biol, 4, e1000102.  
18388201 L.M.Rice, E.A.Montabana, and D.A.Agard (2008).
The lattice as allosteric effector: structural studies of alphabeta- and gamma-tubulin clarify the role of GTP in microtubule assembly.
  Proc Natl Acad Sci U S A, 105, 5378-5383.
PDB code: 3cb2
18024502 S.Huecas, O.Llorca, J.Boskovic, J.Martín-Benito, J.M.Valpuesta, and J.M.Andreu (2008).
Energetics and geometry of FtsZ polymers: nucleated self-assembly of single protofilaments.
  Biophys J, 94, 1796-1806.  
18291323 T.Läppchen, V.A.Pinas, A.F.Hartog, G.J.Koomen, C.Schaffner-Barbero, J.M.Andreu, D.Trambaiolo, J.Löwe, A.Juhem, A.V.Popov, and T.den Blaauwen (2008).
Probing FtsZ and tubulin with C8-substituted GTP analogs reveals differences in their nucleotide binding sites.
  Chem Biol, 15, 189-199.
PDB code: 2r75
18291013 T.den Blaauwen, M.A.de Pedro, M.Nguyen-Distèche, and J.A.Ayala (2008).
Morphogenesis of rod-shaped sacculi.
  FEMS Microbiol Rev, 32, 321-344.  
18515385 Y.Gebremichael, J.W.Chu, and G.A.Voth (2008).
Intrinsic bending and structural rearrangement of tubulin dimer: molecular dynamics simulations and coarse-grained analysis.
  Biophys J, 95, 2487-2499.  
17307852 B.D.Corbin, Y.Wang, T.K.Beuria, and W.Margolin (2007).
Interaction between cell division proteins FtsE and FtsZ.
  J Bacteriol, 189, 3026-3035.  
17468127 D.W.Yoder, D.Kadirjan-Kalbach, B.J.Olson, S.Y.Miyagishima, S.L.Deblasio, R.P.Hangarter, and K.W.Osteryoung (2007).
Effects of mutations in Arabidopsis FtsZ1 on plastid division, FtsZ ring formation and positioning, and FtsZ filament morphology in vivo.
  Plant Cell Physiol, 48, 775-791.  
17563102 H.P.Erickson (2007).
Evolution of the cytoskeleton.
  Bioessays, 29, 668-677.  
17326815 I.Barák, and A.J.Wilkinson (2007).
Division site recognition in Escherichia coli and Bacillus subtilis.
  FEMS Microbiol Rev, 31, 311-326.  
17328675 J.Lutkenhaus (2007).
Assembly dynamics of the bacterial MinCDE system and spatial regulation of the Z ring.
  Annu Rev Biochem, 76, 539-562.  
17493130 P.C.Peters, M.D.Migocki, C.Thoni, and E.J.Harry (2007).
A new assembly pathway for the cytokinetic Z ring from a dynamic helical structure in vegetatively growing cells of Bacillus subtilis.
  Mol Microbiol, 64, 487-499.  
17506674 P.L.Graumann (2007).
Cytoskeletal elements in bacteria.
  Annu Rev Microbiol, 61, 589-618.  
17656575 R.Díaz-Espinoza, A.P.Garcés, J.J.Arbildua, F.Montecinos, J.E.Brunet, R.Lagos, and O.Monasterio (2007).
Domain folding and flexibility of Escherichia coli FtsZ determined by tryptophan site-directed mutagenesis.
  Protein Sci, 16, 1543-1556.  
17977836 S.Huecas, C.Schaffner-Barbero, W.García, H.Yébenes, J.M.Palacios, J.F.Díaz, M.Menéndez, and J.M.Andreu (2007).
The interactions of cell division protein FtsZ with guanine nucleotides.
  J Biol Chem, 282, 37515-37528.  
17644520 Y.Chen, D.E.Anderson, M.Rajagopalan, and H.P.Erickson (2007).
Assembly dynamics of Mycobacterium tuberculosis FtsZ.
  J Biol Chem, 282, 27736-27743.  
17948052 Z.Li, M.J.Trimble, Y.V.Brun, and G.J.Jensen (2007).
The structure of FtsZ filaments in vivo suggests a force-generating role in cell division.
  EMBO J, 26, 4694-4708.  
16987173 A.Briegel, D.P.Dias, Z.Li, R.B.Jensen, A.S.Frangakis, and G.J.Jensen (2006).
Multiple large filament bundles observed in Caulobacter crescentus by electron cryotomography.
  Mol Microbiol, 62, 5.  
16549346 E.Nogales, and H.W.Wang (2006).
Structural mechanisms underlying nucleotide-dependent self-assembly of tubulin and its relatives.
  Curr Opin Struct Biol, 16, 221-229.  
16635801 J.J.Barker (2006).
Antibacterial drug discovery and structure-based design.
  Drug Discov Today, 11, 391-404.  
16756499 K.A.Michie, and J.Löwe (2006).
Dynamic filaments of the bacterial cytoskeleton.
  Annu Rev Biochem, 75, 467-492.  
16484179 K.A.Michie, L.G.Monahan, P.L.Beech, and E.J.Harry (2006).
Trapping of a spiral-like intermediate of the bacterial cytokinetic protein FtsZ.
  J Bacteriol, 188, 1680-1690.  
16959967 Y.L.Shih, and L.Rothfield (2006).
The bacterial cytoskeleton.
  Microbiol Mol Biol Rev, 70, 729-754.  
15967998 D.Schlieper, M.A.Oliva, J.M.Andreu, and J.Löwe (2005).
Structure of bacterial tubulin BtubA/B: evidence for horizontal gene transfer.
  Proc Natl Acad Sci U S A, 102, 9170-9175.
PDB codes: 2bto 2btq
15793307 J.Mingorance, M.Tadros, M.Vicente, J.M.González, G.Rivas, and M.Vélez (2005).
Visualization of single Escherichia coli FtsZ filament dynamics with atomic force microscopy.
  J Biol Chem, 280, 20909-20914.  
15805519 S.D.Redick, J.Stricker, G.Briscoe, and H.P.Erickson (2005).
Mutants of FtsZ targeting the protofilament interface: effects on cell division and GTPase activity.
  J Bacteriol, 187, 2727-2736.  
16227976 W.Margolin (2005).
FtsZ and the division of prokaryotic cells and organelles.
  Nat Rev Mol Cell Biol, 6, 862-871.  
15826938 Y.Chen, and H.P.Erickson (2005).
Rapid in vitro assembly dynamics and subunit turnover of FtsZ demonstrated by fluorescence resonance energy transfer.
  J Biol Chem, 280, 22549-22554.  
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.