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PDBsum entry 2oap
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2oap

 

 

 

 

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Contents
Protein chains
498 a.a. *
Ligands
ANP ×2
Metals
_MG
* Residue conservation analysis
PDB id:
2oap
Name: Hydrolase
Title: Crystal structure of the archaeal secretion atpase gspe in complex with amp-pnp
Structure: Type ii secretion system protein. Chain: 1, 2. Synonym: gspe-2. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 224325. Strain: dsm 4304. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.95Å     R-factor:   0.226     R-free:   0.234
Authors: A.Yamagata,J.A.Tainer
Key ref:
A.Yamagata and J.A.Tainer (2007). Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism. EMBO J, 26, 878-890. PubMed id: 17255937 DOI: 10.1038/sj.emboj.7601544
Date:
17-Dec-06     Release date:   13-Feb-07    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
O29598  (O29598_ARCFU) -  Type II secretion system protein (GspE-2) from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		511 a.a.
498 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1038/sj.emboj.7601544 EMBO J 26:878-890 (2007)
PubMed id: 17255937  
 
 
Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism.
A.Yamagata, J.A.Tainer.
 
  ABSTRACT  
 
The secretion superfamily ATPases are conserved motors in key microbial membrane transport and filament assembly machineries, including bacterial type II and IV secretion, type IV pilus assembly, natural competence, and archaeal flagellae assembly. We report here crystal structures and small angle X-ray scattering (SAXS) solution analyses of the Archaeoglobus fulgidus secretion superfamily ATPase, afGspE. AfGspE structures in complex with ATP analogue AMP-PNP and Mg(2+) reveal for the first time, alternating open and closed subunit conformations within a hexameric ring. The closed-form active site with bound Mg(2+) evidently reveals the catalytically active conformation. Furthermore, nucleotide binding results and SAXS analyses of ADP, ATPgammaS, ADP-Vi, and AMP-PNP-bound states in solution showed that asymmetric assembly involves ADP binding, but clamped closed conformations depend on both ATP gamma-phosphate and Mg(2+) plus the conserved motifs, arginine fingers, and subdomains of the secretion ATPase superfamily. Moreover, protruding N-terminal domain shifts caused by the closed conformation suggest a unified piston-like, push-pull mechanism for ATP hydrolysis-dependent conformational changes, suitable to drive diverse microbial secretion and assembly processes by a universal mechanism.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 AfGspE subunit structure. (A) Experimental electron density (contoured at 1 ) overlaid with the final refined model. (B) AfGspE fold as ribbons (molecule B) with subdomains N1 (yellow), N2 (green), C1 (blue), and C2 (magenta) plus bound AMP-PNP (red sticks), and P-loop (orange, center). (C) Topology schematic, (D) C stereo diagram of two superimposed afGspE subunit structures with bound AMP-PNP (red, CPK spheres). The open form (molecule A, orange) needs NTD rotations to yield the closed form (molecule B, blue). 		Figure 3.
Figure 3 Hexameric ring structure, assembly, AMP-PNP binding, alternating subunit conformations, and subunit interactions. (A) AfGspE hexamer assembly and fold shown as ribbons and as schematic shapes viewed from top and side. Bound AMP-PNP (red, CPK spheres) in closed form molecules (blue, light blue NTD) and alternate open form molecules (orange, light orange NTD). (B) Electron micrograph of negatively stained AfGspE proteins with AMP-PNP. Ring structures are indicated by black arrows. (C) Subunit-subunit interactions with domain colors as in A, and encircled residues for N2:C1 (red), for C1:C1 (green), and N1:C2 (magenta) interactions.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 878-890) 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.  
21234771 B.Zolghadr, A.Klingl, R.Rachel, A.J.Driessen, and S.V.Albers (2011).
The bindosome is a structural component of the Sulfolobus solfataricus cell envelope.
  Extremophiles, 15, 235-244.  
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.  
  20671907 A.F.Ellen, B.Zolghadr, A.M.Driessen, and S.V.Albers (2010).
Shaping the archaeal cell envelope.
  Archaea, 2010, 608243.  
20015340 A.Yamagata, H.Mimura, Y.Sato, M.Yamashita, A.Yoshikawa, and S.Fukai (2010).
Structural insight into the membrane insertion of tail-anchored proteins by Get3.
  Genes Cells, 15, 29-41.
PDB codes: 3a36 3a37
  20976295 K.F.Jarrell, G.M.Jones, and D.B.Nair (2010).
Biosynthesis and role of N-linked glycosylation in cell surface structures of archaea with a focus on flagella and s layers.
  Int J Microbiol, 2010, 470138.  
19620974 G.L.Hura, A.L.Menon, M.Hammel, R.P.Rambo, F.L.Poole, S.E.Tsutakawa, F.E.Jenney, S.Classen, K.A.Frankel, R.C.Hopkins, S.J.Yang, J.W.Scott, B.D.Dillard, M.W.Adams, and J.A.Tainer (2009).
Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS).
  Nat Methods, 6, 606-612.  
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
19347566 S.V.Albers, and M.Pohlschröder (2009).
Diversity of archaeal type IV pilin-like structures.
  Extremophiles, 13, 403-410.  
19609349 T.Doan, C.Morlot, J.Meisner, M.Serrano, A.O.Henriques, C.P.Moran, and D.Z.Rudner (2009).
Novel secretion apparatus maintains spore integrity and developmental gene expression in Bacillus subtilis.
  PLoS Genet, 5, e1000566.  
18257924 E.Parrilli, D.De Vizio, C.Cirulli, and M.L.Tutino (2008).
Development of an improved Pseudoalteromonas haloplanktis TAC125 strain for recombinant protein secretion at low temperature.
  Microb Cell Fact, 7, 2.  
18318657 F.Alber, F.Förster, D.Korkin, M.Topf, and A.Sali (2008).
Integrating diverse data for structure determination of macromolecular assemblies.
  Annu Rev Biochem, 77, 443-477.  
18694757 F.Förster, B.Webb, K.A.Krukenberg, H.Tsuruta, D.A.Agard, and A.Sali (2008).
Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies.
  J Mol Biol, 382, 1089-1106.  
18249533 L.Craig, and J.Li (2008).
Type IV pili: paradoxes in form and function.
  Curr Opin Struct Biol, 18, 267-277.  
18510924 L.Fan, J.O.Fuss, Q.J.Cheng, A.S.Arvai, M.Hammel, V.A.Roberts, P.K.Cooper, and J.A.Tainer (2008).
XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations.
  Cell, 133, 789-800.
PDB codes: 3crv 3crw
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.  
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.  
17887963 B.Chaban, S.Y.Ng, M.Kanbe, I.Saltzman, G.Nimmo, S.Aizawa, and K.F.Jarrell (2007).
Systematic deletion analyses of the fla genes in the flagella operon identify several genes essential for proper assembly and function of flagella in the archaeon, Methanococcus maripaludis.
  Mol Microbiol, 66, 596-609.  
18078545 C.D.Putnam, M.Hammel, G.L.Hura, and J.A.Tainer (2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
  Q Rev Biophys, 40, 191-285.  
18075576 C.V.Robinson, A.Sali, and W.Baumeister (2007).
The molecular sociology of the cell.
  Nature, 450, 973-982.  
17616599 R.F.Collins, M.Saleem, and J.P.Derrick (2007).
Purification and three-dimensional electron microscopy structure of the Neisseria meningitidis type IV pilus biogenesis protein PilG.
  J Bacteriol, 189, 6389-6396.  
17630971 S.J.Shiue, I.L.Chien, N.L.Chan, W.M.Leu, and N.T.Hu (2007).
Mutation of a key residue in the type II secretion system ATPase uncouples ATP hydrolysis from protein translocation.
  Mol Microbiol, 65, 401-412.  
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 codes are shown on the right.

 

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