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PDBsum entry 2wpd

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2wpd
Jmol
Contents
Protein chains
485 a.a. *
470 a.a. *
269 a.a. *
132 a.a. *
59 a.a. *
(+ 4 more) 76 a.a. *
Ligands
ATP ×3
ADP ×2
Metals
_MG ×5
* Residue conservation analysis
PDB id:
2wpd
Name: Hydrolase
Title: The mg.Adp inhibited state of the yeast f1c10 atp synthase
Structure: Atp synthase subunit alpha, mitochondrial. Chain: a, b, c. Synonym: atp synthase alpha chain\, mitochondrial. Atp synthase subunit beta, mitochondrial. Chain: d, e, f. Synonym: atp synthase beta chain\, mitochondrial. Atp synthase subunit gamma, mitochondrial. Chain: g. Synonym: atp synthase gamma chain\,mitochondrial, f-atpase
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: d273-10b/a. Strain: d273-10b/a
Resolution:
3.43Å     R-factor:   0.286     R-free:   0.297
Authors: A.Dautant,J.Velours,M.-F.Giraud
Key ref: A.Dautant et al. (2010). Crystal structure of the Mg·ADP-inhibited state of the yeast F1c10-ATP synthase. J Biol Chem, 285, 29502-29510. PubMed id: 20610387 DOI: 10.1074/jbc.M110.124529
Date:
05-Aug-09     Release date:   07-Jul-10    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07251  (ATPA_YEAST) -  ATP synthase subunit alpha, mitochondrial
Seq:
Struc:
 
Seq:
Struc:
545 a.a.
485 a.a.
Protein chains
Pfam   ArchSchema ?
P00830  (ATPB_YEAST) -  ATP synthase subunit beta, mitochondrial
Seq:
Struc:
511 a.a.
470 a.a.
Protein chain
Pfam   ArchSchema ?
P38077  (ATPG_YEAST) -  ATP synthase subunit gamma, mitochondrial
Seq:
Struc:
311 a.a.
269 a.a.
Protein chain
Pfam   ArchSchema ?
Q12165  (ATPD_YEAST) -  ATP synthase subunit delta, mitochondrial
Seq:
Struc:
160 a.a.
132 a.a.
Protein chain
Pfam   ArchSchema ?
P21306  (ATP5E_YEAST) -  ATP synthase subunit epsilon, mitochondrial
Seq:
Struc:
62 a.a.
59 a.a.
Protein chains
Pfam   ArchSchema ?
P61829  (ATP9_YEAST) -  ATP synthase subunit 9, mitochondrial
Seq:
Struc:
76 a.a.
76 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains D, E, F: 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
Bound ligand (Het Group name = ATP)
corresponds exactly
+ H(2)O
+ H(+)(In)
= ADP
+ phosphate
+ H(+)(Out)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   16 terms 
  Biological process     transport   8 terms 
  Biochemical function     nucleotide binding     10 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M110.124529 J Biol Chem 285:29502-29510 (2010)
PubMed id: 20610387  
 
 
Crystal structure of the Mg·ADP-inhibited state of the yeast F1c10-ATP synthase.
A.Dautant, J.Velours, M.F.Giraud.
 
  ABSTRACT  
 
The F(1)c(10) sub-complex of the yeast F(1)F(0)-ATP synthase includes the membrane rotor part c(10)-ring linked to a catalytic head (alpha/beta)(3) by a central stalk (gammadeltaepsilon). The Saccharomyces cerevisiae yF(1)c(10):ADP sub-complex was crystallized in the presence of Mg.ADP, dicyclohexylcarbodiimide (DCCD) and azide. The structure was solved by molecular replacement using a high resolution model of the yeast F(1) and a bacterial c-ring model with 10 copies of the c-subunit. The structure refined to 3.43 A resolution displays new features compared to the original yF(1)c(10) and to the yF(1) inhibited by adenylyl-imidodiphosphate (AMP-PNP) (yF(1)(I-III)). An ADP molecule was bound in both beta(DP) and beta(TP) catalytic sites. The alpha(DP)-beta (DP) pair is slightly open and resembles the novel conformation identified in yF(1) whereas the alpha (TP)-beta(TP) pair is very closed and resembles more a DP pair. yF(1)c(10) provides a model of a new Mg.ADP-inhibited state of the yeast F(1). Like for the original yF(1) and yF(1)c(10):ADP structures, the foot of the central stalk is rotated by about 40 degrees with respect to bovine structures. The assembly of the F(1) central stalk with the F(0) c-ring rotor is mainly provided by electrostatic interactions. On the rotor ring, the essential cGlu(59) carboxylate group is surrounded by hydrophobic residues and is not involved in hydrogen bonding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
21502534 J.Czub, and H.Grubmüller (2011).
Torsional elasticity and energetics of F1-ATPase.
  Proc Natl Acad Sci U S A, 108, 7408-7413.  
21037553 R.Ishmukhametov, T.Hornung, D.Spetzler, and W.D.Frasch (2010).
Direct observation of stepped proteolipid ring rotation in E. coli F₀F₁-ATP synthase.
  EMBO J, 29, 3911-3923.  
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.