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PDBsum entry 1nge

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Hydrolase(acting on acid anhydrides) PDB id
1nge

 

 

 

 

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Contents
Protein chain
378 a.a. *
Ligands
ATP
Waters ×193
* Residue conservation analysis
PDB id:
1nge
Name: Hydrolase(acting on acid anhydrides)
Title: Structural basis of the 70-kilodalton heat shock cognate protein atp hydrolytic activity, ii. Structure of the active site with adp or atp bound to wild type and mutant atpase fragment
Structure: Heat-shock cognate 70 kd protein. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: brain
Resolution:
2.05Å     R-factor:   0.180    
Authors: K.M.Flaherty,S.M.Wilbanks,C.Deluca-Flaherty,D.B.Mckay
Key ref: K.M.Flaherty et al. (1994). Structural basis of the 70-kilodalton heat shock cognate protein ATP hydrolytic activity. II. Structure of the active site with ADP or ATP bound to wild type and mutant ATPase fragment. J Biol Chem, 269, 12899-12907. PubMed id: 8175707
Date:
17-May-94     Release date:   31-Aug-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P19120  (HSP7C_BOVIN) -  Heat shock cognate 71 kDa protein from Bos taurus
Seq:
Struc:
 
Seq:
Struc:
650 a.a.
378 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.3.6.4.10  - non-chaperonin molecular chaperone ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate + H+
ATP
Bound ligand (Het Group name = ATP)
corresponds exactly
+ H2O
= ADP
+ phosphate
+ H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
J Biol Chem 269:12899-12907 (1994)
PubMed id: 8175707  
 
 
Structural basis of the 70-kilodalton heat shock cognate protein ATP hydrolytic activity. II. Structure of the active site with ADP or ATP bound to wild type and mutant ATPase fragment.
K.M.Flaherty, S.M.Wilbanks, C.DeLuca-Flaherty, D.B.McKay.
 
  ABSTRACT  
 
The ATPase fragment of the bovine 70-kDa heat shock cognate protein is an attractive construct in which to study its mechanism of ATP hydrolysis. The three-dimensional structure suggests several residues that might participate in the ATPase reaction. Four acidic residues (Asp-10, Glu-175, Asp-199, and Asp-206) have been individually mutated to both the cognate amine (asparagine/glutamine) and to serine, and the effects of the mutations on the kinetics of the ATPase activity (Wilbanks, S. M., DeLuca-Flaherty, C., and McKay, D. B. (1994) J. Biol. Chem. 269, 12893-12898) and the structure of the mutant ATPase fragments have been determined, typically to approximately 2.4 A resolution. Additionally, the structures of the wild type protein complexed with MgADP and Pi, MgAMPPNP (5'-adenylyl-beta, gamma-imidodiphosphate) and CaAMPPNP have been refined to 2.1, 2.4, and 2.4 A, respectively. Combined, these structures provide models for the prehydrolysis, MgATP-bound state and the post-hydrolysis, MgADP-bound state of the ATPase fragment. These models suggest a pathway for the hydrolytic reaction in which 1) the gamma phosphate of bound ATP reorients to form a beta, gamma-bidentate phosphate complex with the Mg2+ ion, allowing 2) in-line nucleophilic attack on the gamma phosphate by a H2O molecule or OH- ion, with 3) subsequent release of inorganic phosphate.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21482798 A.Zhuravleva, and L.M.Gierasch (2011).
Allosteric signal transmission in the nucleotide-binding domain of 70-kDa heat shock protein (Hsp70) molecular chaperones.
  Proc Natl Acad Sci U S A, 108, 6987-6992.  
20179333 M.Shida, A.Arakawa, R.Ishii, S.Kishishita, T.Takagi, M.Kukimoto-Niino, S.Sugano, A.Tanaka, M.Shirouzu, and S.Yokoyama (2010).
Direct inter-subdomain interactions switch between the closed and open forms of the Hsp70 nucleotide-binding domain in the nucleotide-free state.
  Acta Crystallogr D Biol Crystallogr, 66, 223-232.
PDB codes: 2e88 2e8a
19361428 A.Bhattacharya, A.V.Kurochkin, G.N.Yip, Y.Zhang, E.B.Bertelsen, and E.R.Zuiderweg (2009).
Allostery in Hsp70 chaperones is transduced by subdomain rotations.
  J Mol Biol, 388, 475-490.  
19439666 E.B.Bertelsen, L.Chang, J.E.Gestwicki, and E.R.Zuiderweg (2009).
Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate.
  Proc Natl Acad Sci U S A, 106, 8471-8476.
PDB code: 2kho
19883127 H.J.Woo, J.Jiang, E.M.Lafer, and R.Sousa (2009).
ATP-induced conformational changes in Hsp70: molecular dynamics and experimental validation of an in silico predicted conformation.
  Biochemistry, 48, 11470-11477.  
19759005 J.de Keyzer, G.J.Steel, S.J.Hale, D.Humphries, and C.J.Stirling (2009).
Nucleotide binding by Lhs1p is essential for its nucleotide exchange activity and for function in vivo.
  J Biol Chem, 284, 31564-31571.  
19444470 K.W.Modisakeng, M.Jiwaji, E.R.Pesce, J.Robert, C.T.Amemiya, R.A.Dorrington, and G.L.Blatch (2009).
Isolation of a Latimeria menadoensis heat shock protein 70 (Lmhsp70) that has all the features of an inducible gene and encodes a functional molecular chaperone.
  Mol Genet Genomics, 282, 185-196.  
18550409 J.P.Schuermann, J.Jiang, J.Cuellar, O.Llorca, L.Wang, L.E.Gimenez, S.Jin, A.B.Taylor, B.Demeler, K.A.Morano, P.J.Hart, J.M.Valpuesta, E.M.Lafer, and R.Sousa (2008).
Structure of the Hsp110:Hsc70 nucleotide exchange machine.
  Mol Cell, 31, 232-243.
PDB code: 3c7n
18458329 M.Zebisch, and N.Sträter (2008).
Structural insight into signal conversion and inactivation by NTPDase2 in purinergic signaling.
  Proc Natl Acad Sci U S A, 105, 6882-6887.
PDB codes: 3cj1 3cj7 3cj9 3cja
17434124 J.F.Swain, G.Dinler, R.Sivendran, D.L.Montgomery, M.Stotz, and L.M.Gierasch (2007).
Hsp70 chaperone ligands control domain association via an allosteric mechanism mediated by the interdomain linker.
  Mol Cell, 26, 27-39.  
17996706 J.Jiang, E.G.Maes, A.B.Taylor, L.Wang, A.P.Hinck, E.M.Lafer, and R.Sousa (2007).
Structural basis of J cochaperone binding and regulation of Hsp70.
  Mol Cell, 28, 422-433.
PDB codes: 2qw9 2qwl 2qwm 2qwn 2qwo 2qwp 2qwq 2qwr
17923091 Q.Liu, and W.A.Hendrickson (2007).
Insights into Hsp70 chaperone activity from a crystal structure of the yeast Hsp110 Sse1.
  Cell, 131, 106-120.
PDB code: 2qxl
  16511258 J.Jiang, E.M.Lafer, and R.Sousa (2006).
Crystallization of a functionally intact Hsc70 chaperone.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 39-43.  
16455491 M.Vogel, B.Bukau, and M.P.Mayer (2006).
Allosteric regulation of Hsp70 chaperones by a proline switch.
  Mol Cell, 21, 359-367.  
17026666 R.Sousa, and E.M.Lafer (2006).
Keep the traffic moving: mechanism of the Hsp70 motor.
  Traffic, 7, 1596-1603.  
16307916 J.Jiang, K.Prasad, E.M.Lafer, and R.Sousa (2005).
Structural basis of interdomain communication in the Hsc70 chaperone.
  Mol Cell, 20, 513-524.
PDB code: 1yuw
15618627 K.Kawasaki, T.Shibata, and F.Ito (2004).
Roles of the HSP70-subunit in a eukaryotic multi-site-specific endonuclease, Endo.SceI: autophosphorylation and heat stability.
  Biosci Biotechnol Biochem, 68, 2557-2564.  
12517345 D.I.Liao, L.Reiss, I.Turner, and G.Dotson (2003).
Structure of glycerol dehydratase reactivase: a new type of molecular chaperone.
  Structure, 11, 109-119.
PDB code: 1nbw
12932733 N.N.Alder, and S.M.Theg (2003).
Energy use by biological protein transport pathways.
  Trends Biochem Sci, 28, 442-451.  
14553940 T.Hansen, and P.Schönheit (2003).
ATP-dependent glucokinase from the hyperthermophilic bacterium Thermotoga maritima represents an extremely thermophilic ROK glucokinase with high substrate specificity.
  FEMS Microbiol Lett, 226, 405-411.  
12419215 C.W.Carter, and W.L.Duax (2002).
Did tRNA synthetase classes arise on opposite strands of the same gene?
  Mol Cell, 10, 705-708.  
12374829 T.Hansen, B.Reichstein, R.Schmid, and P.Schönheit (2002).
The first archaeal ATP-dependent glucokinase, from the hyperthermophilic crenarchaeon Aeropyrum pernix, represents a monomeric, extremely thermophilic ROK glucokinase with broad hexose specificity.
  J Bacteriol, 184, 5955-5965.  
11544208 T.K.Barthel, J.Zhang, and G.C.Walker (2001).
ATPase-defective derivatives of Escherichia coli DnaK that behave differently with respect to ATP-induced conformational change and peptide release.
  J Bacteriol, 183, 5482-5490.  
10866806 H.Schüler, M.Nyåkern, C.E.Schutt, U.Lindberg, and R.Karlsson (2000).
Mutational analysis of arginine 177 in the nucleotide binding site of beta-actin.
  Eur J Biochem, 267, 4054-4062.  
10878579 L.A.Boyer, and C.L.Peterson (2000).
Actin-related proteins (Arps): conformational switches for chromatin-remodeling machines?
  Bioessays, 22, 666-672.  
10090737 C.E.Bystrom, D.W.Pettigrew, B.P.Branchaud, P.O'Brien, and S.J.Remington (1999).
Crystal structures of Escherichia coli glycerol kinase variant S58-->W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion.
  Biochemistry, 38, 3508-3518.
PDB codes: 1bwf 1glj 1gll
  10397752 F.Elefant, and K.B.Palter (1999).
Tissue-specific expression of dominant negative mutant Drosophila HSC70 causes developmental defects and lethality.
  Mol Biol Cell, 10, 2101-2117.  
10373003 K.Pawłowski, B.Zhang, L.Rychlewski, and A.Godzik (1999).
The Helicobacter pylori genome: from sequence analysis to structural and functional predictions.
  Proteins, 36, 20-30.  
10223297 W.Wriggers, and K.Schulten (1999).
Investigating a back door mechanism of actin phosphate release by steered molecular dynamics.
  Proteins, 35, 262-273.  
9476895 B.Bukau, and A.L.Horwich (1998).
The Hsp70 and Hsp60 chaperone machines.
  Cell, 92, 351-366.  
9463376 L.Esser, C.R.Wang, M.Hosaka, C.S.Smagula, T.C.Südhof, and J.Deisenhofer (1998).
Synapsin I is structurally similar to ATP-utilizing enzymes.
  EMBO J, 17, 977-984.
PDB codes: 1auv 1aux
9585559 S.M.Wilbanks, and D.B.McKay (1998).
Structural replacement of active site monovalent cations by the epsilon-amino group of lysine in the ATPase fragment of bovine Hsc70.
  Biochemistry, 37, 7456-7462.
PDB codes: 1ba0 1ba1
9454592 S.V.Slepenkov, and S.N.Witt (1998).
Kinetics of the reactions of the Escherichia coli molecular chaperone DnaK with ATP: evidence that a three-step reaction precedes ATP hydrolysis.
  Biochemistry, 37, 1015-1024.  
9585537 T.Rajapandi, C.Wu, E.Eisenberg, and L.Greene (1998).
Characterization of D10S and K71E mutants of human cytosolic hsp70.
  Biochemistry, 37, 7244-7250.  
9675167 W.Wriggers, and K.Schulten (1998).
Nucleotide-dependent movements of the kinesin motor domain predicted by simulated annealing.
  Biophys J, 75, 646-661.  
9230303 C.Prodromou, S.M.Roe, R.O'Brien, J.E.Ladbury, P.W.Piper, and L.H.Pearl (1997).
Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone.
  Cell, 90, 65-75.
PDB codes: 1a4h 1am1 1amw
9083109 M.Sriram, J.Osipiuk, B.Freeman, R.Morimoto, and A.Joachimiak (1997).
Human Hsp70 molecular chaperone binds two calcium ions within the ATPase domain.
  Structure, 5, 403-414.
PDB code: 1s3x
9251782 W.Wriggers, and K.Schulten (1997).
Stability and dynamics of G-actin: back-door water diffusion and behavior of a subdomain 3/4 loop.
  Biophys J, 73, 624-639.  
8855953 C.Zeng, A.E.Aleshin, J.B.Hardie, R.W.Harrison, and H.J.Fromm (1996).
ATP-binding site of human brain hexokinase as studied by molecular modeling and site-directed mutagenesis.
  Biochemistry, 35, 13157-13164.  
8922377 S.E.Holstein, H.Ungewickell, and E.Ungewickell (1996).
Mechanism of clathrin basket dissociation: separate functions of protein domains of the DnaJ homologue auxilin.
  J Cell Biol, 135, 925-937.  
7773752 F.U.Hartl, and J.Martin (1995).
Molecular chaperones in cellular protein folding.
  Curr Opin Struct Biol, 5, 92.  
  7612964 L.M.Hendershot, J.Y.Wei, J.R.Gaut, B.Lawson, P.J.Freiden, and K.G.Murti (1995).
In vivo expression of mammalian BiP ATPase mutants causes disruption of the endoplasmic reticulum.
  Mol Biol Cell, 6, 283-296.  
8078940 D.B.Bivin, K.Ue, M.Khoroshev, and M.Morales (1994).
Effect of lysine methylation and other ATPase modulators on the active site of myosin subfragment 1.
  Proc Natl Acad Sci U S A, 91, 8665-8669.  
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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