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PDBsum entry 2zbf

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protein ligands metals links
Hydrolase PDB id
2zbf
Jmol PyMol
Contents
Protein chain
995 a.a. *
Ligands
BEF
TG1
Metals
_MG
Waters ×311
* Residue conservation analysis
PDB id:
2zbf
Name: Hydrolase
Title: Calcium pump crystal structure with bound bef3 and tg in the of calcium
Structure: Sarcoplasmic/endoplasmic reticulum calcium atpase chain: a. Synonym: calcium pump 1, serca1, sr ca(2+)-atpase 1, calciu transporting atpase sarcoplasmic reticulum type, fast twitc muscle isoform, endoplasmic reticulum class 1/2 ca(2+) atpa ec: 3.6.3.8
Source: Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Tissue: skeletal muscle (white)
Resolution:
2.40Å     R-factor:   0.212     R-free:   0.257
Authors: C.Toyoshima,H.Ogawa,Y.Norimatsu
Key ref:
C.Toyoshima et al. (2007). How processing of aspartylphosphate is coupled to lumenal gating of the ion pathway in the calcium pump. Proc Natl Acad Sci U S A, 104, 19831-19836. PubMed id: 18077416 DOI: 10.1073/pnas.0709978104
Date:
20-Oct-07     Release date:   11-Dec-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04191  (AT2A1_RABIT) -  Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Seq:
Struc:
 
Seq:
Struc:
1001 a.a.
994 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.6.3.8  - Calcium-transporting ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + Ca2+(Side 1) = ADP + phosphate + Ca2+(Side 2)
ATP
+ H(2)O
+ Ca(2+)(Side 1)
= ADP
+ phosphate
+ Ca(2+)(Side 2)
      Cofactor: Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   6 terms 
  Biological process     transport   6 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0709978104 Proc Natl Acad Sci U S A 104:19831-19836 (2007)
PubMed id: 18077416  
 
 
How processing of aspartylphosphate is coupled to lumenal gating of the ion pathway in the calcium pump.
C.Toyoshima, Y.Norimatsu, S.Iwasawa, T.Tsuda, H.Ogawa.
 
  ABSTRACT  
 
Ca(2+)-ATPase of skeletal muscle sarcoplasmic reticulum is the best-studied member of the P-type or E1/E2 type ion transporting ATPases. It has been crystallized in seven different states that cover nearly the entire reaction cycle. Here we describe the structure of this ATPase complexed with phosphate analogs BeF(3)(-) and AlF(4)(-) in the absence of Ca(2+), which correspond to the E2P ground state and E2 approximately P transition state, respectively. The luminal gate is open with BeF(3)(-) and closed with AlF(4)(-). These and the E1 approximately P.ADP analog crystal structures show that a two-step rotation of the cytoplasmic A-domain opens and closes the luminal gate through the movements of the M1-M4 transmembrane helices. There are several conformational switches coupled to the rotation, and the one in the cytoplasmic part of M2 has critical importance. In the second step of rotation, positioning of one water molecule couples the hydrolysis of aspartylphosphate to closing of the gate.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Cross-sections of the transmembrane region of Ca^2+-ATPase. van der Waals surfaces of E1·AlF ·ADP (a) and E2·BeF (–TG) (b). Red colors represent acidic residues. Dotted circles in b indicate the positions of Ca^2+ observed in E1·AlF ·ADP (a). The images shown were prepared with PyMol (34).
Figure 7.
Fig. 7. A cartoon illustrating two-step rotation in the processing of aspartylphosphate and gating of the ion pathway. Small arrows indicate the movements of the TM helices. The M1–M4 (green) and A1–A3 (yellow) helices are numbered. P-D351 refers to phosphorylated Asp-351.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21239683 C.Toyoshima, S.Yonekura, J.Tsueda, and S.Iwasawa (2011).
Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca2+-ATPase in the absence of Ca2+.
  Proc Natl Acad Sci U S A, 108, 1833-1838.
PDB codes: 3ar2 3ar3 3ar4 3ar5 3ar6 3ar7 3ar8 3ar9
21118704 D.H.Maclennan, and E.Zvaritch (2011).
Mechanistic models for muscle diseases and disorders originating in the sarcoplasmic reticulum.
  Biochim Biophys Acta, 1813, 948-964.  
21179061 J.P.Morth, B.P.Pedersen, M.J.Buch-Pedersen, J.P.Andersen, B.Vilsen, M.G.Palmgren, and P.Nissen (2011).
A structural overview of the plasma membrane Na+,K+-ATPase and H+-ATPase ion pumps.
  Nat Rev Mol Cell Biol, 12, 60-70.  
  21224846 K.Abe, K.Tani, and Y.Fujiyoshi (2011).
Conformational rearrangement of gastric H(+),K(+)-ATPase induced by an acid suppressant.
  Nat Commun, 2, 155.
PDB code: 2xzb
20118641 H.Suzuki, K.Yamasaki, T.Daiho, and S.Danko (2010).
Mechanism of ca(2+) pump as revealed by mutations, development of stable analogs of phosphorylated intermediates, and their structural analyses.
  Yakugaku Zasshi, 130, 179-189.  
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.  
20634056 M.Bublitz, H.Poulsen, J.P.Morth, and P.Nissen (2010).
In and out of the cation pumps: P-type ATPase structure revisited.
  Curr Opin Struct Biol, 20, 431-439.  
  20548052 N.Vedovato, and D.C.Gadsby (2010).
The two C-terminal tyrosines stabilize occluded Na/K pump conformations containing Na or K ions.
  J Gen Physiol, 136, 63-82.  
21098671 Y.Sugita, M.Ikeguchi, and C.Toyoshima (2010).
Relationship between Ca2+-affinity and shielding of bulk water in the Ca2+-pump from molecular dynamics simulations.
  Proc Natl Acad Sci U S A, 107, 21465-21469.  
  19806033 A.Takeuchi, N.Reyes, P.Artigas, and D.C.Gadsby (2009).
Visualizing the mapped ion pathway through the Na,K-ATPase pump.
  Channels (Austin), 3, 383-386.  
19780839 C.Völlmecke, C.Kötting, K.Gerwert, and M.Lübben (2009).
Spectroscopic investigation of the reaction mechanism of CopB-B, the catalytic fragment from an archaeal thermophilic ATP-driven heavy metal transporter.
  FEBS J, 276, 6172-6186.  
19339978 D.C.Gadsby (2009).
Ion channels versus ion pumps: the principal difference, in principle.
  Nat Rev Mol Cell Biol, 10, 344-352.  
19666591 H.Ogawa, T.Shinoda, F.Cornelius, and C.Toyoshima (2009).
Crystal structure of the sodium-potassium pump (Na+,K+-ATPase) with bound potassium and ouabain.
  Proc Natl Acad Sci U S A, 106, 13742-13747.
PDB code: 3a3y
  19255470 K.O.Håkansson, and A.Curović (2009).
Crystallization and data collection of the nucleotide-binding domain of Mg-ATPase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 223-225.  
19621894 R.D.Peluffo, R.M.González-Lebrero, S.B.Kaufman, S.Kortagere, B.Orban, R.C.Rossi, and J.R.Berlin (2009).
Quaternary benzyltriethylammonium ion binding to the Na,K-ATPase: a tool to investigate extracellular K+ binding reactions.
  Biochemistry, 48, 8105-8119.  
19561071 S.Danko, T.Daiho, K.Yamasaki, X.Liu, and H.Suzuki (2009).
Formation of the stable structural analog of ADP-sensitive phosphoenzyme of Ca2+-ATPase with occluded Ca2+ by beryllium fluoride: structural changes during phosphorylation and isomerization.
  J Biol Chem, 284, 22722-22735.  
19628462 X.Liu, T.Daiho, K.Yamasaki, G.Wang, S.Danko, and H.Suzuki (2009).
Roles of interaction between actuator and nucleotide binding domains of sarco(endo)plasmic reticulum Ca(2+)-ATPase as revealed by single and swap mutational analyses of serine 186 and glutamate 439.
  J Biol Chem, 284, 25190-25198.  
19364131 Y.Hatori, D.Lewis, C.Toyoshima, and G.Inesi (2009).
Reaction cycle of Thermotoga maritima copper ATPase and conformational characterization of catalytically deficient mutants.
  Biochemistry, 48, 4871-4880.  
18849964 A.Takeuchi, N.Reyes, P.Artigas, and D.C.Gadsby (2008).
The ion pathway through the opened Na(+),K(+)-ATPase pump.
  Nature, 456, 413-416.  
18728008 K.Yamasaki, G.Wang, T.Daiho, S.Danko, and H.Suzuki (2008).
Roles of Tyr122-hydrophobic cluster and K+ binding in Ca2+ -releasing process of ADP-insensitive phosphoenzyme of sarcoplasmic reticulum Ca2+ -ATPase.
  J Biol Chem, 283, 29144-29155.  
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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