PDBsum entry 2hld

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Hydrolase PDB id
Protein chains
(+ 3 more) 482 a.a. *
(+ 3 more) 470 a.a. *
265 a.a. *
120 a.a. *
48 a.a. *
243 a.a. *
84 a.a. *
34 a.a. *
200 a.a. *
17 a.a. *
27 a.a. *
ANP ×15
_MG ×15
Waters ×183
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of yeast mitochondrial f1-atpase
Structure: Atp synthase alpha chain, mitochondrial. Chain: a, b, c, j, k, l, s, t, u. Atp synthase beta chain, mitochondrial. Chain: d, e, f, m, n, o, v, w, x. Engineered: yes. Atp synthase gamma chain, mitochondrial. Chain: g, p, y. Atp synthase delta chain, mitochondrial. Chain: h, q, z.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organelle: mitochondria. Gene: atp2. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Organelle: mitochondria
Biol. unit: Nonamer (from PQS)
2.80Å     R-factor:   0.207     R-free:   0.244
Authors: V.Kabaleeswaran,N.Puri,J.E.Walker,A.G.Leslie,D.M.Mueller
Key ref:
V.Kabaleeswaran et al. (2006). Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1 ATPase. EMBO J, 25, 5433-5442. PubMed id: 17082766 DOI: 10.1038/sj.emboj.7601410
06-Jul-06     Release date:   28-Nov-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P07251  (ATPA_YEAST) -  ATP synthase subunit alpha, mitochondrial
545 a.a.
482 a.a.
Protein chains
Pfam   ArchSchema ?
P00830  (ATPB_YEAST) -  ATP synthase subunit beta, mitochondrial
511 a.a.
470 a.a.
Protein chain
Pfam   ArchSchema ?
P38077  (ATPG_YEAST) -  ATP synthase subunit gamma, mitochondrial
311 a.a.
265 a.a.
Protein chain
Pfam   ArchSchema ?
Q12165  (ATPD_YEAST) -  ATP synthase subunit delta, mitochondrial
160 a.a.
120 a.a.
Protein chain
Pfam   ArchSchema ?
P21306  (ATP5E_YEAST) -  ATP synthase subunit epsilon, mitochondrial
62 a.a.
48 a.a.
Protein chain
Pfam   ArchSchema ?
P38077  (ATPG_YEAST) -  ATP synthase subunit gamma, mitochondrial
311 a.a.
243 a.a.
Protein chain
Pfam   ArchSchema ?
Q12165  (ATPD_YEAST) -  ATP synthase subunit delta, mitochondrial
160 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P21306  (ATP5E_YEAST) -  ATP synthase subunit epsilon, mitochondrial
62 a.a.
34 a.a.
Protein chain
Pfam   ArchSchema ?
P38077  (ATPG_YEAST) -  ATP synthase subunit gamma, mitochondrial
311 a.a.
200 a.a.
Protein chain
Pfam   ArchSchema ?
Q12165  (ATPD_YEAST) -  ATP synthase subunit delta, mitochondrial
160 a.a.
17 a.a.
Protein chain
Pfam   ArchSchema ?
P21306  (ATP5E_YEAST) -  ATP synthase subunit epsilon, mitochondrial
62 a.a.
27 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.  - H(+)-transporting two-sector ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + H+(In) = ADP + phosphate + H+(Out)
+ H(2)O
+ H(+)(In)
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
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  


DOI no: 10.1038/sj.emboj.7601410 EMBO J 25:5433-5442 (2006)
PubMed id: 17082766  
Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1 ATPase.
V.Kabaleeswaran, N.Puri, J.E.Walker, A.G.Leslie, D.M.Mueller.
The crystal structure of yeast mitochondrial F(1) ATPase contains three independent copies of the complex, two of which have similar conformations while the third differs in the position of the central stalk relative to the alpha(3)beta(3) sub-assembly. All three copies display very similar asymmetric features to those observed for the bovine enzyme, but the yeast F(1) ATPase structures provide novel information. In particular, the active site that binds ADP in bovine F(1) ATPase has an ATP analog bound and therefore this structure does not represent the ADP-inhibited form. In addition, one of the complexes binds phosphate in the nucleotide-free catalytic site, and comparison with other structures provides a picture of the movement of the phosphate group during initial binding and subsequent catalysis. The shifts in position of the central stalk between two of the three copies of yeast F(1) ATPase and when these structures are compared to those of the bovine enzyme give new insight into the conformational changes that take place during rotational catalysis.
  Selected figure(s)  
Figure 3.
Figure 3 Phosphate-binding site in the [E]-subunit of the yF[1]II complex. (A) Electron density of the final 2F[o]-F[c] map for the phosphate-binding site (contoured at 1.3 ). The electron density is shown only for a radius about the phosphate to simplify the image. (B) Side chains that contribute to phosphate binding. Possible ionic interactions are shown as dotted lines, with distances in Å. (C) Superposition of the phosphate-binding region of yF[1]I (green) on that of yF[1]II (blue). (D) Superposition of the phosphate-binding region of the empty subunit of bovine F[1] (pink) on yF[1]II (blue). The bovine residue numbering is used in this image.
Figure 5.
Figure 5 Relative movement of the phosphate molecule during the catalytic cycle. The predicted path of the phosphate molecule during catalysis is marked by the position of phosphate (or sulfate) in the [E]-subunits of the yF[1]II complex (blue), the bovine AlF[4]^-:ADP-inhibited structure (Menz et al, 2001) (yellow), and the -phosphate of AMPPNP bound to the [DP]-subunit of the yF[1]I complex (salmon). The structures were superimposed using the P-loop and neighboring catalytic residues ( 151–177, 330–336). The -carbon trace of the P-loop of all three enzymes is shown along with the bound nucleotide and phosphate (or sulfate) of yF[1]II (yellow). The inset shows just the movement of the phosphate relative to the nucleotide. The phosphate bound to [E] (blue) moves to the position in the AlF[4]^-:ADP-inhibited state (yellow) and ends as the -phosphate of ATP in the DP site (as colored). Also shown is the movement of Arg375 in the same path. The distances between the atoms are shown in Å.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 5433-5442) copyright 2006.  
  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 F(1)-ATPase: Interplay among Enzyme Structures, Catalysis, and Rotations.
  Structure, 19, 588-598.  
19933271 A.Meulemans, S.Seneca, T.Pribyl, J.Smet, V.Alderweirldt, A.Waeytens, W.Lissens, R.Van Coster, L.De Meirleir, J.P.di Rago, D.L.Gatti, and S.H.Ackerman (2010).
Defining the pathogenesis of the human Atp12p W94R mutation using a Saccharomyces cerevisiae yeast model.
  J Biol Chem, 285, 4099-4109.  
20809990 J.V.Møller, C.Olesen, A.M.Winther, and P.Nissen (2010).
The sarcoplasmic Ca2+-ATPase: design of a perfect chemi-osmotic pump.
  Q Rev Biophys, 43, 501-566.  
20035080 L.A.Kane, M.J.Youngman, R.E.Jensen, and J.E.Van Eyk (2010).
Phosphorylation of the F(1)F(o) ATP synthase beta subunit: functional and structural consequences assessed in a model system.
  Circ Res, 106, 504-513.  
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.  
20871600 R.Watanabe, R.Iino, and H.Noji (2010).
Phosphate release in F1-ATPase catalytic cycle follows ADP release.
  Nat Chem Biol, 6, 814-820.  
20100509 T.F.Laughlin, and Z.Ahmad (2010).
Inhibition of Escherichia coli ATP synthase by amphibian antimicrobial peptides.
  Int J Biol Macromol, 46, 367-374.  
20370611 V.V.Bulygin, and Y.M.Milgrom (2010).
Probes of inhibition of Escherichia coli F(1)-ATPase by 7-chloro-4-nitrobenz-2-oxa-1,3-diazole in the presence of MgADP and MgATP support a bi-site mechanism of ATP hydrolysis by the enzyme.
  Biochemistry (Mosc), 75, 327-335.  
19383603 A.Ludlam, J.Brunzelle, T.Pribyl, X.Xu, D.L.Gatti, and S.H.Ackerman (2009).
Chaperones of F1-ATPase.
  J Biol Chem, 284, 17138-17146.
PDB codes: 2r31 2zd2
19995987 D.M.Rees, A.G.Leslie, and J.E.Walker (2009).
The structure of the membrane extrinsic region of bovine ATP synthase.
  Proc Natl Acad Sci U S A, 106, 21597-21601.
PDB code: 2wss
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.  
19348765 J.G.Wise, and P.D.Vogel (2009).
Accommodating discontinuities in dimeric left-handed coiled coils in ATP synthase external stalks.
  Biophys J, 96, 2823-2831.  
19893485 M.J.Maher, S.Akimoto, M.Iwata, K.Nagata, Y.Hori, M.Yoshida, S.Yokoyama, S.Iwata, and K.Yokoyama (2009).
Crystal structure of A3B3 complex of V-ATPase from Thermus thermophilus.
  EMBO J, 28, 3771-3779.
PDB code: 3gqb
19233840 V.Kabaleeswaran, H.Shen, J.Symersky, J.E.Walker, A.G.Leslie, and D.M.Mueller (2009).
Asymmetric structure of the yeast f1 ATPase in the absence of bound nucleotides.
  J Biol Chem, 284, 10546-10551.
PDB code: 3fks
19280602 W.Zheng (2009).
Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase.
  Proteins, 76, 747-762.  
18846414 A.F.Lodeyro, M.V.Castelli, and O.A.Roveri (2008).
ATP hydrolysis-driven H(+) translocation is stimulated by sulfate, a strong inhibitor of mitochondrial ATP synthesis.
  J Bioenerg Biomembr, 40, 269-279.  
18380897 A.Y.Mulkidjanian, M.Y.Galperin, K.S.Makarova, Y.I.Wolf, and E.V.Koonin (2008).
Evolutionary primacy of sodium bioenergetics.
  Biol Direct, 3, 13.  
18485887 A.Y.Mulkidjanian, P.Dibrov, and M.Y.Galperin (2008).
The past and present of sodium energetics: may the sodium-motive force be with you.
  Biochim Biophys Acta, 1777, 985-992.  
19075235 D.Okuno, R.Fujisawa, R.Iino, Y.Hirono-Hara, H.Imamura, and H.Noji (2008).
Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation.
  Proc Natl Acad Sci U S A, 105, 20722-20727.  
18721138 D.Pogoryelov, Y.Nikolaev, U.Schlattner, K.Pervushin, P.Dimroth, and T.Meier (2008).
Probing the rotor subunit interface of the ATP synthase from Ilyobacter tartaricus.
  FEBS J, 275, 4850-4862.  
18819926 H.Shen, D.E.Walters, and D.M.Mueller (2008).
Introduction of the chloroplast redox regulatory region in the yeast ATP synthase impairs cytochrome C oxidase.
  J Biol Chem, 283, 32937-32943.  
18723591 H.Sielaff, H.Rennekamp, S.Engelbrecht, and W.Junge (2008).
Functional halt positions of rotary FOF1-ATPase correlated with crystal structures.
  Biophys J, 95, 4979-4987.  
18957411 J.K.Ramalingam, C.Hunke, X.Gao, G.Grüber, and P.R.Preiser (2008).
ATP/ADP Binding to a Novel Nucleotide Binding Domain of the Reticulocyte-binding Protein Py235 of Plasmodium yoelii.
  J Biol Chem, 283, 36386-36396.  
18216260 J.Pu, and M.Karplus (2008).
How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase.
  Proc Natl Acad Sci U S A, 105, 1192-1197.  
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.  
18276891 S.Furuike, M.D.Hossain, Y.Maki, K.Adachi, T.Suzuki, A.Kohori, H.Itoh, M.Yoshida, and K.Kinosita (2008).
Axle-less F1-ATPase rotates in the correct direction.
  Science, 319, 955-958.  
19011636 T.Masaike, F.Koyama-Horibe, K.Oiwa, M.Yoshida, and T.Nishizaka (2008).
Cooperative three-step motions in catalytic subunits of F(1)-ATPase correlate with 80 degrees and 40 degrees substep rotations.
  Nat Struct Mol Biol, 15, 1326-1333.  
17698806 J.R.Gledhill, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2007).
Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols.
  Proc Natl Acad Sci U S A, 104, 13632-13637.
PDB codes: 2jiz 2jj1 2jj2
17662945 K.Adachi, K.Oiwa, T.Nishizaka, S.Furuike, H.Noji, H.Itoh, M.Yoshida, and K.Kinosita (2007).
Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation.
  Cell, 130, 309-321.  
17350959 M.W.Bowler, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2007).
Ground state structure of F1-ATPase from bovine heart mitochondria at 1.9 A resolution.
  J Biol Chem, 282, 14238-14242.
PDB code: 2jdi
17244612 Y.Wang, U.Singh, and D.M.Mueller (2007).
Mitochondrial genome integrity mutations uncouple the yeast Saccharomyces cerevisiae ATP synthase.
  J Biol Chem, 282, 8228-8236.  
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.