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PDBsum entry 3fks

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
3fks
Jmol
Contents
Protein chains
(+ 3 more) 484 a.a. *
(+ 3 more) 466 a.a. *
268 a.a. *
116 a.a. *
46 a.a. *
235 a.a. *
68 a.a. *
25 a.a. *
187 a.a. *
11 a.a. *
25 a.a. *
Ligands
PO4 ×15
* Residue conservation analysis
PDB id:
3fks
Name: Hydrolase
Title: Yeast f1 atpase in the absence of bound nucleotides
Structure: Atp synthase subunit alpha, mitochondrial. Chain: a, b, c, j, k, l, s, t, u. Fragment: unp residues 36-545. Atp synthase subunit beta, mitochondrial. Chain: d, e, f, m, n, o, v, w, x. Fragment: unp residues 34-511. Engineered: yes. Atp synthase subunit gamma, mitochondrial. Chain: g, p, y.
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Organelle: mitochondria. Gene: atp2, j2041, yjr121w. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Organelle: mitochondria
Resolution:
3.59Å     R-factor:   0.243     R-free:   0.306
Authors: V.Kabaleeswaran,J.Symersky,H.Shen,J.E.Walker,A.G.W.Leslie, D.M.Mueller
Key ref:
V.Kabaleeswaran et al. (2009). Asymmetric structure of the yeast F1 ATPase in the absence of bound nucleotides. J Biol Chem, 284, 10546-10551. PubMed id: 19233840 DOI: 10.1074/jbc.M900544200
Date:
17-Dec-08     Release date:   03-Mar-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07251  (ATPA_YEAST) -  ATP synthase subunit alpha, mitochondrial
Seq:
Struc:
 
Seq:
Struc:
545 a.a.
484 a.a.
Protein chains
Pfam   ArchSchema ?
P00830  (ATPB_YEAST) -  ATP synthase subunit beta, mitochondrial
Seq:
Struc:
511 a.a.
466 a.a.
Protein chain
Pfam   ArchSchema ?
P38077  (ATPG_YEAST) -  ATP synthase subunit gamma, mitochondrial
Seq:
Struc:
311 a.a.
268 a.a.
Protein chain
Pfam   ArchSchema ?
Q12165  (ATPD_YEAST) -  ATP synthase subunit delta, mitochondrial
Seq:
Struc:
160 a.a.
116 a.a.
Protein chain
Pfam   ArchSchema ?
P21306  (ATP5E_YEAST) -  ATP synthase subunit epsilon, mitochondrial
Seq:
Struc:
62 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P38077  (ATPG_YEAST) -  ATP synthase subunit gamma, mitochondrial
Seq:
Struc:
311 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
Q12165  (ATPD_YEAST) -  ATP synthase subunit delta, mitochondrial
Seq:
Struc:
160 a.a.
68 a.a.
Protein chain
Pfam   ArchSchema ?
P21306  (ATP5E_YEAST) -  ATP synthase subunit epsilon, mitochondrial
Seq:
Struc:
62 a.a.
25 a.a.
Protein chain
Pfam   ArchSchema ?
P38077  (ATPG_YEAST) -  ATP synthase subunit gamma, mitochondrial
Seq:
Struc:
311 a.a.
187 a.a.
Protein chain
Pfam   ArchSchema ?
Q12165  (ATPD_YEAST) -  ATP synthase subunit delta, mitochondrial
Seq:
Struc:
160 a.a.
11 a.a.
Protein chain
Pfam   ArchSchema ?
P21306  (ATP5E_YEAST) -  ATP synthase subunit epsilon, mitochondrial
Seq:
Struc:
62 a.a.
25 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains D, E, F, M, N, O, V, W, X: E.C.3.6.3.14  - H(+)-transporting two-sector ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + H+(In) = ADP + phosphate + H+(Out)
ATP
+ H(2)O
+ H(+)(In)
= ADP
+
phosphate
Bound ligand (Het Group name = PO4)
corresponds exactly
+ H(+)(Out)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   11 terms 
  Biological process     transport   8 terms 
  Biochemical function     hydrolase activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M900544200 J Biol Chem 284:10546-10551 (2009)
PubMed id: 19233840  
 
 
Asymmetric structure of the yeast F1 ATPase in the absence of bound nucleotides.
V.Kabaleeswaran, H.Shen, J.Symersky, J.E.Walker, A.G.Leslie, D.M.Mueller.
 
  ABSTRACT  
 
The crystal structure of nucleotide-free yeast F(1) ATPase has been determined at a resolution of 3.6 A. The overall structure is very similar to that of the ground state enzyme. In particular, the beta(DP) and beta(TP) subunits both adopt the closed conformation found in the ground state structure despite the absence of bound nucleotides. This implies that interactions between the gamma and beta subunits are as important as nucleotide occupancy in determining the conformational state of the beta subunits. Furthermore, this result suggests that for the mitochondrial enzyme, there is no state of nucleotide occupancy that would result in more than one of the beta subunits adopting the open conformation. The adenine-binding pocket of the beta(TP) subunit is disrupted in the apoenzyme, suggesting that the beta(DP) subunit is responsible for unisite catalytic activity.
 
  Selected figure(s)  
 
Figure 1.
Electron density at the catalytic sites of yeast F[1] ATPase in the absence of nucleotides. In each panel, the 2F[o] - F[c] map is shown (contoured at 1 σ) with the position of the nucleotide modeled from the ground state structure. The inset plots show the region where the nucleotide would bind and corresponding electron density. The main chain is represented as a ribbon in red and blue for the α and β subunits, respectively. The side chains of selected residues important for substrate binding and catalysis are shown. A, α[DP]/β[DP] site; B, α[TP]/β[TP] site; C, a noncatalytic (NC) site, all for Complex I. D, the phosphate-binding site in the α[E]/β[E] site of Complex II.
Figure 3.
Electron density maps calculated with regions of the model omitted. Stereo images showing the electron density omit maps calculated excluding residues βVal-371–Leu-391 (A) and βSer-340–Pro-350, and βGlu-422–Pro-428 (B) along with the pertinent regions of the final model are shown. The 2F[o] - F[c] maps are contoured at 1 σ.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 10546-10551) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23334411 S.Arai, S.Saijo, K.Suzuki, K.Mizutani, Y.Kakinuma, Y.Ishizuka-Katsura, N.Ohsawa, T.Terada, M.Shirouzu, S.Yokoyama, S.Iwata, I.Yamato, and T.Murata (2013).
Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures.
  Nature, 493, 703-707.
PDB codes: 3vr2 3vr3 3vr4 3vr5 3vr6
22504883 J.Symersky, V.Pagadala, D.Osowski, A.Krah, T.Meier, J.D.Faraldo-Gómez, and D.M.Mueller (2012).
Structure of the c(10) ring of the yeast mitochondrial ATP synthase in the open conformation.
  Nat Struct Mol Biol, 19, 485.
PDB codes: 3u2f 3u2y 3u32 3ud0
21602818 G.Cingolani, and T.M.Duncan (2011).
Structure of the ATP synthase catalytic complex (F(1)) from Escherichia coli in an autoinhibited conformation.
  Nat Struct Mol Biol, 18, 701-707.  
21481781 K.Okazaki, and S.Takada (2011).
Structural comparison of F1-ATPase: interplay among enzyme structures, catalysis, and rotations.
  Structure, 19, 588-598.  
20371322 R.Shimo-Kon, E.Muneyuki, H.Sakai, K.Adachi, M.Yoshida, and K.Kinosita (2010).
Chemo-mechanical coupling in F(1)-ATPase revealed by catalytic site occupancy during catalysis.
  Biophys J, 98, 1227-1236.  
20689227 Y.Kagawa (2010).
ATP synthase: from single molecule to human bioenergetics.
  Proc Jpn Acad Ser B Phys Biol Sci, 86, 667-693.  
19821035 J.C.Talbot, A.Dautant, A.Polidori, B.Pucci, T.Cohen-Bouhacina, A.Maali, B.Salin, D.Brèthes, J.Velours, and M.F.Giraud (2009).
Hydrogenated and fluorinated surfactants derived from Tris(hydroxymethyl)-acrylamidomethane allow the purification of a highly active yeast F1-F0 ATP-synthase with an enhanced stability.
  J Bioenerg Biomembr, 41, 349-360.  
19779483 N.Numoto, Y.Hasegawa, K.Takeda, and K.Miki (2009).
Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase.
  EMBO Rep, 10, 1228-1234.
PDB codes: 3a5c 3a5d
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.