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PDBsum entry 1ank

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protein ligands Protein-protein interface(s) links
Transferase(phosphotransferase) PDB id
1ank
Jmol
Contents
Protein chains
214 a.a. *
Ligands
AMP ×2
ANP ×2
Waters ×533
* Residue conservation analysis
PDB id:
1ank
Name: Transferase(phosphotransferase)
Title: The closed conformation of a highly flexible protein: the structure of e. Coli adenylate kinase with bound amp and amppnp
Structure: Adenylate kinase. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Resolution:
2.00Å     R-factor:   0.201     R-free:   0.316
Authors: M.B.Berry,B.Meador,T.Bilderback,P.Liang,M.Glaser, G.N.Phillips Jr.
Key ref: M.B.Berry et al. (1994). The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP. Proteins, 19, 183-198. PubMed id: 7937733
Date:
28-Feb-94     Release date:   31-May-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P69441  (KAD_ECOLI) -  Adenylate kinase
Seq:
Struc:
214 a.a.
214 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.4.3  - Adenylate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + AMP = 2 ADP
ATP
+
AMP
Bound ligand (Het Group name = AMP)
corresponds exactly
=
2 × ADP
Bound ligand (Het Group name = ANP)
matches with 81.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     AMP salvage   10 terms 
  Biochemical function     nucleotide binding     10 terms  

 

 
    reference    
 
 
Proteins 19:183-198 (1994)
PubMed id: 7937733  
 
 
The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP.
M.B.Berry, B.Meador, T.Bilderback, P.Liang, M.Glaser, G.N.Phillips.
 
  ABSTRACT  
 
The structure of E. coli adenylate kinase with bound AMP and AMPPNP at 2.0 A resolution is presented. The protein crystallizes in space group C2 with two molecules in the asymmetric unit, and has been refined to an R factor of 20.1% and an Rfree of 31.6%. In the present structure, the protein is in the closed (globular) form with the large flexible lid domain covering the AMPPNP molecule. Within the protein, AMP and AMPPNP, and ATP analog, occupy the AMP and ATP sites respectively, which had been suggested by the most recent crystal structure of E. coli adenylate kinase with Ap5A bound (Müller and Schulz, 1992, ref. 1) and prior fluorescence studies (Liang et al., 1991, ref. 2). The binding of substrates and the positions of the active site residues are compared between the present structure and the E. coli adenylate kinase/Ap5A structure. We failed to detect a peak in the density map corresponding to the Mg2+ ion which is required for catalysis, and its absence has been attributed to the use of ammonium sulfate in the crystallization solution. Finally, a comparison is made between the present structure and the structure of the heavy chain of muscle myosin.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21183988 Y.W.Tan, and H.Yang (2011).
Seeing the forest for the trees: fluorescence studies of single enzymes in the context of ensemble experiments.
  Phys Chem Chem Phys, 13, 1709-1721.  
19751742 O.Beckstein, E.J.Denning, J.R.Perilla, and T.B.Woolf (2009).
Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.
  J Mol Biol, 394, 160-176.  
19130895 R.Liu, A.L.Ström, J.Zhai, J.Gal, S.Bao, W.Gong, and H.Zhu (2009).
Enzymatically inactive adenylate kinase 4 interacts with mitochondrial ADP/ATP translocase.
  Int J Biochem Cell Biol, 41, 1371-1380.  
19805283 Y.Araiso, R.L.Sherrer, R.Ishitani, J.M.Ho, D.Söll, and O.Nureki (2009).
Structure of a tRNA-dependent kinase essential for selenocysteine decoding.
  Proc Natl Acad Sci U S A, 106, 16215-16220.
PDB codes: 3a4l 3a4m 3a4n
18676657 N.Kantarci-Carsibasi, T.Haliloglu, and P.Doruker (2008).
Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes.
  Biophys J, 95, 5862-5873.  
18805924 Q.Dong, C.O.Randak, and M.J.Welsh (2008).
A mutation in CFTR modifies the effects of the adenylate kinase inhibitor Ap5A on channel gating.
  Biophys J, 95, 5178-5185.  
18174226 R.L.Sherrer, P.O'Donoghue, and D.Söll (2008).
Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation.
  Nucleic Acids Res, 36, 1247-1259.  
17299745 C.Snow, G.Qi, and S.Hayward (2007).
Essential dynamics sampling study of adenylate kinase: comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions.
  Proteins, 67, 325-337.  
17989222 J.A.Hanson, K.Duderstadt, L.P.Watkins, S.Bhattacharyya, J.Brokaw, J.W.Chu, and H.Yang (2007).
Illuminating the mechanistic roles of enzyme conformational dynamics.
  Proc Natl Acad Sci U S A, 104, 18055-18060.  
17960260 J.S.Salafsky (2007).
Second-harmonic generation for studying structural motion of biological molecules in real time and space.
  Phys Chem Chem Phys, 9, 5704-5711.  
16302237 M.B.Berry, E.Bae, T.R.Bilderback, M.Glaser, and G.N.Phillips (2006).
Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase.
  Proteins, 62, 555-556.
PDB code: 2eck
16672241 M.Bellinzoni, A.Haouz, M.Graña, H.Munier-Lehmann, W.Shepard, and P.M.Alzari (2006).
The crystal structure of Mycobacterium tuberculosis adenylate kinase in complex with two molecules of ADP and Mg2+ supports an associative mechanism for phosphoryl transfer.
  Protein Sci, 15, 1489-1493.
PDB code: 2cdn
15521058 H.Krishnamurthy, H.Lou, A.Kimple, C.Vieille, and R.I.Cukier (2005).
Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates.
  Proteins, 58, 88.  
15735347 L.Lehtiö, I.Fabrichniy, T.Hansen, P.Schönheit, and A.Goldman (2005).
Unusual twinning in an acetyl coenzyme A synthetase (ADP-forming) from Pyrococcus furiosus.
  Acta Crystallogr D Biol Crystallogr, 61, 350-354.  
15972825 T.Hibino (2005).
Nonfixed relationship of the Michaelis constant and maximum velocity with their corresponding rate constants.
  J Biol Chem, 280, 30671-30680.  
15281134 D.B.Sherman, S.Zhang, J.B.Pitner, and A.Tropsha (2004).
Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method.
  Proteins, 56, 828-838.  
14754987 J.H.Eastberg, J.Pelletier, and B.L.Stoddard (2004).
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.
  Nucleic Acids Res, 32, 653-660.
PDB codes: 1rc8 1rpz 1rrc
15116357 M.Lei, M.I.Zavodszky, L.A.Kuhn, and M.F.Thorpe (2004).
Sampling protein conformations and pathways.
  J Comput Chem, 25, 1133-1148.  
15334070 M.Wolf-Watz, V.Thai, K.Henzler-Wildman, G.Hadjipavlou, E.Z.Eisenmesser, and D.Kern (2004).
Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair.
  Nat Struct Mol Biol, 11, 945-949.  
15382240 N.A.Temiz, E.Meirovitch, and I.Bahar (2004).
Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data.
  Proteins, 57, 468-480.  
15229886 N.Fernandez-Fuentes, A.Hermoso, J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2004).
Classification of common functional loops of kinase super-families.
  Proteins, 56, 539-555.  
14556639 R.S.Mani, F.Karimi-Busheri, M.Fanta, C.E.Cass, and M.Weinfeld (2003).
Spectroscopic studies of DNA and ATP binding to human polynucleotide kinase: evidence for a ternary complex.
  Biochemistry, 42, 12077-12084.  
12220496 E.A.Galburt, J.Pelletier, G.Wilson, and B.L.Stoddard (2002).
Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase.
  Structure, 10, 1249-1260.
PDB code: 1ltq
12036965 N.Sekulic, L.Shuvalova, O.Spangenberg, M.Konrad, and A.Lavie (2002).
Structural characterization of the closed conformation of mouse guanylate kinase.
  J Biol Chem, 277, 30236-30243.
PDB code: 1lvg
11325743 S.Kumar, Y.Y.Sham, C.J.Tsai, and R.Nussinov (2001).
Protein folding and function: the N-terminal fragment in adenylate kinase.
  Biophys J, 80, 2439-2454.  
11123913 I.M.Li de La Sierra, J.Gallay, M.Vincent, T.Bertrand, P.Briozzo, O.Bârzu, and A.M.Gilles (2000).
Substrate-induced fit of the ATP binding site of cytidine monophosphate kinase from Escherichia coli: time-resolved fluorescence of 3'-anthraniloyl-2'-deoxy-ADP and molecular modeling.
  Biochemistry, 39, 15870-15878.  
10873853 N.Ostermann, I.Schlichting, R.Brundiers, M.Konrad, J.Reinstein, T.Veit, R.S.Goody, and A.Lavie (2000).
Insights into the phosphoryltransfer mechanism of human thymidylate kinase gained from crystal structures of enzyme complexes along the reaction coordinate.
  Structure, 8, 629-642.
PDB codes: 1e2d 1e2e 1e2f 1e2g 1e2q
10508782 C.H.Weber, Y.S.Park, S.Sanker, C.Kent, and M.L.Ludwig (1999).
A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from bacillus subtilis.
  Structure, 7, 1113-1124.
PDB code: 1coz
10450084 S.Hayward (1999).
Structural principles governing domain motions in proteins.
  Proteins, 36, 425-435.  
9826650 A.Lavie, N.Ostermann, R.Brundiers, R.S.Goody, J.Reinstein, M.Konrad, and I.Schlichting (1998).
Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase.
  Proc Natl Acad Sci U S A, 95, 14045-14050.
PDB codes: 4tmk 5tmp
9593186 B.L.de Groot, S.Hayward, D.M.van Aalten, A.Amadei, and H.J.Berendsen (1998).
Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.
  Proteins, 31, 116-127.  
9715904 M.B.Berry, and G.N.Phillips (1998).
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+.
  Proteins, 32, 276-288.
PDB codes: 1zin 1zio 1zip
9668095 S.Burlacu-Miron, V.Perrier, A.M.Gilles, E.Pistotnik, and C.T.Craescu (1998).
Structural and energetic factors of the increased thermal stability in a genetically engineered Escherichia coli adenylate kinase.
  J Biol Chem, 273, 19102-19107.  
9144797 P.Haney, J.Konisky, K.K.Koretke, Z.Luthey-Schulten, and P.G.Wolynes (1997).
Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus.
  Proteins, 28, 117-130.  
9235932 Y.Zhang, Y.Li, Y.Wu, and H.Yan (1997).
Structural and functional roles of tyrosine 78 of yeast guanylate kinase.
  J Biol Chem, 272, 19343-19350.  
  8670851 A.Teplyakov, P.Sebastiao, G.Obmolova, A.Perrakis, G.S.Brush, M.J.Bessman, and K.S.Wilson (1996).
Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
  EMBO J, 15, 3487-3497.
PDB codes: 1dek 1del
8785318 C.A.Smith, and I.Rayment (1996).
Active site comparisons highlight structural similarities between myosin and other P-loop proteins.
  Biophys J, 70, 1590-1602.  
8805521 C.W.Müller, G.J.Schlauderer, J.Reinstein, and G.E.Schulz (1996).
Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding.
  Structure, 4, 147-156.
PDB code: 4ake
  8868479 G.J.Schlauderer, and G.E.Schulz (1996).
The structure of bovine mitochondrial adenylate kinase: comparison with isoenzymes in other compartments.
  Protein Sci, 5, 434-441.
PDB codes: 1ak2 2ak2
  8976551 G.S.Prasad, E.A.Stura, D.E.McRee, G.S.Laco, C.Hasselkus-Light, J.H.Elder, and C.D.Stout (1996).
Crystal structure of dUTP pyrophosphatase from feline immunodeficiency virus.
  Protein Sci, 5, 2429-2437.
PDB code: 1dut
8650159 Q.Lu, and M.Inouye (1996).
Adenylate kinase complements nucleoside diphosphate kinase deficiency in nucleotide metabolism.
  Proc Natl Acad Sci U S A, 93, 5720-5725.  
7893717 C.L.Careaga, J.Sutherland, J.Sabeti, and J.J.Falke (1995).
Large amplitude twisting motions of an interdomain hinge: a disulfide trapping study of the galactose-glucose binding protein.
  Biochemistry, 34, 3048-3055.  
  7618889 J.Konisky, P.C.Michels, and D.S.Clark (1995).
Pressure stabilization is not a general property of thermophilic enzymes: the adenylate kinases of Methanococcus voltae, Methanococcus maripaludis, Methanococcus thermolithotrophicus, and Methanococcus jannaschii.
  Appl Environ Microbiol, 61, 2762-2764.  
  7768791 P.Rusnak, P.Haney, and J.Konisky (1995).
The adenylate kinases from a mesophilic and three thermophilic methanogenic members of the Archaea.
  J Bacteriol, 177, 2977-2981.  
  7795532 R.Sowdhamini, and T.L.Blundell (1995).
An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins.
  Protein Sci, 4, 506-520.  
  7670369 U.Abele, and G.E.Schulz (1995).
High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer.
  Protein Sci, 4, 1262-1271.
PDB codes: 1aky 2aky
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.