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PDBsum entry 2eww

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Protein transport PDB id
2eww
Jmol
Contents
Protein chain
343 a.a. *
Ligands
ATP
Waters ×2
* Residue conservation analysis
PDB id:
2eww
Name: Protein transport
Title: Crystal structure of the pilus retraction motor pilt and bound atp
Structure: Twitching motility protein pilt. Chain: a. Engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PDB file)
Resolution:
3.20Å     R-factor:   0.242     R-free:   0.310
Authors: K.A.Satyshur,K.T.Forest
Key ref:
K.A.Satyshur et al. (2007). Crystal structures of the pilus retraction motor PilT suggest large domain movements and subunit cooperation drive motility. Structure, 15, 363-376. PubMed id: 17355871 DOI: 10.1016/j.str.2007.01.018
Date:
07-Nov-05     Release date:   21-Nov-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O66950  (O66950_AQUAE) -  Twitching motility protein PilT
Seq:
Struc:
366 a.a.
343 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1016/j.str.2007.01.018 Structure 15:363-376 (2007)
PubMed id: 17355871  
 
 
Crystal structures of the pilus retraction motor PilT suggest large domain movements and subunit cooperation drive motility.
K.A.Satyshur, G.A.Worzalla, L.S.Meyer, E.K.Heiniger, K.G.Aukema, A.M.Misic, K.T.Forest.
 
  ABSTRACT  
 
PilT is a hexameric ATPase required for bacterial type IV pilus retraction and surface motility. Crystal structures of ADP- and ATP-bound Aquifex aeolicus PilT at 2.8 and 3.2 A resolution show N-terminal PAS-like and C-terminal RecA-like ATPase domains followed by a set of short C-terminal helices. The hexamer is formed by extensive polar subunit interactions between the ATPase core of one monomer and the N-terminal domain of the next. An additional structure captures a nonsymmetric PilT hexamer in which approach of invariant arginines from two subunits to the bound nucleotide forms an enzymatically competent active site. A panel of pilT mutations highlights the importance of the arginines, the PAS-like domain, the polar subunit interface, and the C-terminal helices for retraction. We present a model for ATP binding leading to dramatic PilT domain motions, engagement of the arginine wire, and subunit communication in this hexameric motor. Our conclusions apply to the entire type II/IV secretion ATPase family.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Conserved Elements of PilT Fold
(A) The NTD of PilT (colored as in Figure 2A) resembles the well-known PAS domain (gray, represented by the circadian clock protein Period; Yildiz et al., 2005). Noncanonical PAS elements (PilT αA and loops within Period) are removed for clarity.
(B) The core ATPase subdomain of PilT (green) is readily superimposable upon RecA (Story and Steitz, 1992) (gray). In this view, the least-squares calculation is over P-loop residues only. Type II/IV secretion ATPase family motifs Walker A (blue), Asp box (lime green), Walker B (magenta), and His box (orange) neighbor the bound nucleotide.
(C) Isolated, magnified view of the four sequence motifs described in (B), with ATP and signature invariant residues Lys149, Glu176, Glu217, and His242 depicted (blue, green, magenta, and orange, respectively).
Figure 8.
Figure 8. Model for Concerted PilT Motions
(A) The quasi-two-fold symmetric C2 crystal structure has two peripheral wide-open subunits (B, E; blue), two central “active” subunits (C, F; orange), and two central “resting” subunits (A, D; green). Four CTD:CTD interfaces are engaged (double lines). The remaining two are disengaged (zig-zag). Subunit F is clamped around bound nucleotide.
(B) When ATP (red) binds in the E cleft, the two domains close around the ligand (short black arrows), causing the β5/β6 arginines to approach the ATP. Because of the extensive CTD[D]:NTD[E] interface, the motion of NTD[E] forces the swiveling of CTD[D](in particular the C-terminal helices) toward the periphery of the hexamer (long gray arrow). Consequently, the D arginine fingers approach the E active site (double lines). On the other side of CTD[D], the interface likewise rearranges, disengaging CTD[C] from the D active site (zig-zag).
(C) Subunit D is now poised as the most peripheral, wide-open subunit and ready to bind nucleotide; E is clamped around nucleotide and contributing to an engaged CTD:CTD interface on either side.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2007, 15, 363-376) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22466878 K.V.Korotkov, M.Sandkvist, and W.G.Hol (2012).
The type II secretion system: biogenesis, molecular architecture and mechanism.
  Nat Rev Microbiol, 10, 336-351.  
21255118 M.D.Gray, M.Bagdasarian, W.G.Hol, and M.Sandkvist (2011).
In vivo cross-linking of EpsG to EpsL suggests a role for EpsL as an ATPase-pseudopilin coupling protein in the Type II secretion system of Vibrio cholerae.
  Mol Microbiol, 79, 786-798.  
20482147 C.Holz, D.Opitz, L.Greune, R.Kurre, M.Koomey, M.A.Schmidt, and B.Maier (2010).
Multiple pilus motors cooperate for persistent bacterial movement in two dimensions.
  Phys Rev Lett, 104, 178104.  
20439474 D.R.Brown, S.Helaine, E.Carbonnelle, and V.Pelicic (2010).
Systematic functional analysis reveals that a set of seven genes is involved in fine-tuning of the multiple functions mediated by type IV pili in Neisseria meningitidis.
  Infect Immun, 78, 3053-3063.  
20722599 M.Ayers, P.L.Howell, and L.L.Burrows (2010).
Architecture of the type II secretion and type IV pilus machineries.
  Future Microbiol, 5, 1203-1218.  
19775250 I.Bulyha, C.Schmidt, P.Lenz, V.Jakovljevic, A.Höne, B.Maier, M.Hoppert, and L.Søgaard-Andersen (2009).
Regulation of the type IV pili molecular machine by dynamic localization of two motor proteins.
  Mol Microbiol, 74, 691-706.  
19646531 J.Abendroth, A.C.Kreger, and W.G.Hol (2009).
The dimer formed by the periplasmic domain of EpsL from the Type 2 Secretion System of Vibrio parahaemolyticus.
  J Struct Biol, 168, 313-322.
PDB code: 2w7v
19186152 M.Clausen, M.Koomey, and B.Maier (2009).
Dynamics of type IV pili is controlled by switching between multiple states.
  Biophys J, 96, 1169-1177.  
18605899 D.Kaiser (2008).
Myxococcus-from single-cell polarity to complex multicellular patterns.
  Annu Rev Genet, 42, 109-130.  
18165299 J.B.Goldberg, R.E.Hancock, R.E.Parales, J.Loper, and P.Cornelis (2008).
Pseudomonas 2007.
  J Bacteriol, 190, 2649-2662.  
18461074 K.F.Jarrell, and M.J.McBride (2008).
The surprisingly diverse ways that prokaryotes move.
  Nat Rev Microbiol, 6, 466-476.  
18249533 L.Craig, and J.Li (2008).
Type IV pili: paradoxes in form and function.
  Curr Opin Struct Biol, 18, 267-277.  
18416602 N.Biais, B.Ladoux, D.Higashi, M.So, and M.Sheetz (2008).
Cooperative retraction of bundled type IV pili enables nanonewton force generation.
  PLoS Biol, 6, e87.  
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.  
18668121 R.Fronzes, H.Remaut, and G.Waksman (2008).
Architectures and biogenesis of non-flagellar protein appendages in Gram-negative bacteria.
  EMBO J, 27, 2271-2280.  
18223089 V.Jakovljevic, S.Leonardy, M.Hoppert, and L.Søgaard-Andersen (2008).
PilB and PilT are ATPases acting antagonistically in type IV pilus function in Myxococcus xanthus.
  J Bacteriol, 190, 2411-2421.  
18399938 V.Pelicic (2008).
Type IV pili: e pluribus unum?
  Mol Microbiol, 68, 827-837.  
18310333 X.Han, R.M.Kennan, J.K.Davies, L.A.Reddacliff, O.P.Dhungyel, R.J.Whittington, L.Turnbull, C.B.Whitchurch, and J.I.Rood (2008).
Twitching motility is essential for virulence in Dichelobacter nodosus.
  J Bacteriol, 190, 3323-3335.  
18006497 X.Ma, N.Sayed, P.Baskaran, A.Beuve, and F.van den Akker (2008).
PAS-mediated dimerization of soluble guanylyl cyclase revealed by signal transduction histidine kinase domain crystal structure.
  J Biol Chem, 283, 1167-1178.
PDB codes: 2p04 2p08
17637359 D.Kaiser (2007).
Bacterial swarming: a re-examination of cell-movement patterns.
  Curr Biol, 17, R561-R570.  
17355860 S.N.Savvides (2007).
Secretion superfamily ATPases swing big.
  Structure, 15, 255-257.  
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.