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protein ligands metals links
Transferase PDB id
1p3j
Jmol
Contents
Protein chain
212 a.a. *
Ligands
AP5
Metals
_ZN
_MG
Waters ×139
* Residue conservation analysis
PDB id:
1p3j
Name: Transferase
Title: Adenylate kinase from bacillus subtilis
Structure: Adenylate kinase. Chain: a. Synonym: atp-amp transphosphorylase, superoxide-inducible protein 16, soi16. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: adk. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.197     R-free:   0.246
Authors: E.Bae,G.N.Phillips Jr.
Key ref:
E.Bae and G.N.Phillips (2004). Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases. J Biol Chem, 279, 28202-28208. PubMed id: 15100224 DOI: 10.1074/jbc.M401865200
Date:
17-Apr-03     Release date:   04-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P16304  (KAD_BACSU) -  Adenylate kinase
Seq:
Struc: 		217 a.a.
212 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
Bound ligand (Het Group name = AP5)
matches with 54.00% similarity 		+ AMP
 = 2 × ADP
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     nucleobase, nucleoside, nucleotide and nucleic acid metabolic process   2 terms 
  Biochemical function     nucleotide binding     9 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M401865200 J Biol Chem 279:28202-28208 (2004)
PubMed id: 15100224  
 
 
Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases.
E.Bae, G.N.Phillips.
 
  ABSTRACT  
 
The crystal structures of adenylate kinases from the psychrophile Bacillus globisporus and the mesophile Bacillus subtilis have been solved and compared with that from the thermophile Bacillus stearothermophilus. This is the first example we know of where a trio of protein structures has been solved that have the same number of amino acids and a high level of identity (66-74%) and yet come from organisms with different operating temperatures. The enzymes were characterized for their own thermal denaturation and inactivation, and they exhibited the same temperature preferences as their source organisms. The structures of the three highly homologous, dynamic proteins with different temperature-activity profiles provide an opportunity to explore a molecular mechanism of cold and heat adaptation. Their analysis suggests that the maintenance of the balance between stability and flexibility is crucial for proteins to function at their environmental temperatures, and it is achieved by the modification of intramolecular interactions in the process of temperature adaptation.
 
  Selected figure(s)  
 
Figure 4.
FIG. 4. Zn2+ coordination in AKsub. The zinc ion is ligated to three Cys and one Asp. The structure of this arrangement is revealed for the first time in this study. The zinc coordination is virtually identical in AKglo and AKsub structures. Electron density at the 1 contour level is shown with the Zn2+ atom (shown in orange) and its four liganding residues. 		Figure 6.
FIG. 6. Effect of residue 179 substitution on hydrophobic interactions in Bacillus AKs. In AKste the side chain of Met-179 fits into a hydrophobic pocket made by Met-6, Gly-7, and Leu-8, resulting in the burial of hydrophobic surface. Residues 6-8 and 179 of AKglo, AKsub, and AKste are shown as blue, green, and red stick models, respectively. Multiple conformers of Thr-179 of AKsub are all shown. Water molecules in AKglo and AKsub are represented at the center as blue and green spheres, respectively.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 28202-28208) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20821240 A.Mukhopadhyay, A.V.Kladova, S.A.Bursakov, O.Y.Gavel, J.J.Calvete, V.L.Shnyrov, I.Moura, J.J.Moura, M.J.Romão, and J.Trincão (2011).
Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria.
  J Biol Inorg Chem, 16, 51-61.
PDB codes: 2xb4 3l0p 3l0s
20980336 B.Cobucci-Ponzano, G.Perugino, M.Rossi, and M.Moracci (2011).
Engineering the stability and the activity of a glycoside hydrolase.
  Protein Eng Des Sel, 24, 21-26.  
21436043 E.Gonzales-Vigil, C.M.Bianchetti, G.N.Phillips, and G.A.Howe (2011).
Adaptive evolution of threonine deaminase in plant defense against insect herbivores.
  Proc Natl Acad Sci U S A, 108, 5897-5902.
PDB code: 3iau
20631681 M.I.Peña, M.Davlieva, M.R.Bennett, J.S.Olson, and Y.Shamoo (2010).
Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection.
  Mol Syst Biol, 6, 387.  
20418388 P.Q.Nguyen, and J.J.Silberg (2010).
A selection that reports on protein-protein interactions within a thermophilic bacterium.
  Protein Eng Des Sel, 23, 529-536.  
19181663 B.B.Xie, F.Bian, X.L.Chen, H.L.He, J.Guo, X.Gao, Y.X.Zeng, B.Chen, B.C.Zhou, and Y.Z.Zhang (2009).
Cold adaptation of zinc metalloproteases in the thermolysin family from deep sea and arctic sea ice bacteria revealed by catalytic and structural properties and molecular dynamics: new insights into relationship between conformational flexibility and hydrogen bonding.
  J Biol Chem, 284, 9257-9269.  
19408959 K.Ratcliff, J.Corn, and S.Marqusee (2009).
Structure, stability, and folding of ribonuclease H1 from the moderately thermophilic Chlorobium tepidum: comparison with thermophilic and mesophilic homologues.
  Biochemistry, 48, 5890-5898.
PDB code: 3h08
19397279 L.Qin, J.Liu, D.A.Mills, D.A.Proshlyakov, C.Hiser, and S.Ferguson-Miller (2009).
Redox-dependent conformational changes in cytochrome C oxidase suggest a gating mechanism for proton uptake.
  Biochemistry, 48, 5121-5130.
PDB codes: 3fye 3fyi
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.  
18780158 A.K.Williamson (2008).
Structural and functional aspects of the MSP (PsbO) and study of its differences in thermophilic versus mesophilic organisms.
  Photosynth Res, 98, 365-389.  
18312599 C.Michaux, J.Massant, F.Kerff, J.M.Frère, J.D.Docquier, I.Vandenberghe, B.Samyn, A.Pierrard, G.Feller, P.Charlier, J.Van Beeumen, and J.Wouters (2008).
Crystal structure of a cold-adapted class C beta-lactamase.
  FEBS J, 275, 1687-1697.
PDB code: 2qz6
18621726 E.Bae, R.M.Bannen, and G.N.Phillips (2008).
Bioinformatic method for protein thermal stabilization by structural entropy optimization.
  Proc Natl Acad Sci U S A, 105, 9594-9597.  
17222185 B.Altermark, L.Niiranen, N.P.Willassen, A.O.Smalås, and E.Moe (2007).
Comparative studies of endonuclease I from cold-adapted Vibrio salmonicida and mesophilic Vibrio cholerae.
  FEBS J, 274, 252-263.  
17623850 B.Tamames, S.F.Sousa, J.Tamames, P.A.Fernandes, and M.J.Ramos (2007).
Analysis of zinc-ligand bond lengths in metalloproteins: trends and patterns.
  Proteins, 69, 466-475.  
17195087 J.C.Marx, T.Collins, S.D'Amico, G.Feller, and C.Gerday (2007).
Cold-adapted enzymes from marine Antarctic microorganisms.
  Mar Biotechnol (NY), 9, 293-304.  
17576517 S.Thorvaldsen, E.Hjerde, C.Fenton, and N.P.Willassen (2007).
Molecular characterization of cold adaptation based on ortholog protein sequences from Vibrionaceae species.
  Extremophiles, 11, 719-732.  
17235516 V.Spiwok, P.Lipovová, T.Skálová, J.Dusková, J.Dohnálek, J.Hasek, N.J.Russell, and B.Králová (2007).
Cold-active enzymes studied by comparative molecular dynamics simulation.
  J Mol Model, 13, 485-497.  
16452168 E.Bae, and G.N.Phillips (2006).
Roles of static and dynamic domains in stability and catalysis of adenylate kinase.
  Proc Natl Acad Sci U S A, 103, 2132-2137.  
16705665 K.S.Siddiqui, A.Poljak, M.Guilhaus, D.De Francisci, P.M.Curmi, G.Feller, S.D'Amico, C.Gerday, V.N.Uversky, and R.Cavicchioli (2006).
Role of lysine versus arginine in enzyme cold-adaptation: modifying lysine to homo-arginine stabilizes the cold-adapted alpha-amylase from Pseudoalteramonas haloplanktis.
  Proteins, 64, 486-501.  
16756497 K.S.Siddiqui, and R.Cavicchioli (2006).
Cold-adapted enzymes.
  Annu Rev Biochem, 75, 403-433.  
15670163 J.Arnórsdóttir, M.M.Kristjánsson, and R.Ficner (2005).
Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation.
  FEBS J, 272, 832-845.
PDB codes: 1s2n 1sh7
15935511 M.Kilstrup, K.Hammer, P.Ruhdal Jensen, and J.Martinussen (2005).
Nucleotide metabolism and its control in lactic acid bacteria.
  FEMS Microbiol Rev, 29, 555-590.  
  16233714 A.Hoyoux, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.L.Huston, J.C.Marx, G.Sonan, Y.Zeng, G.Feller, and C.Gerday (2004).
Extreme catalysts from low-temperature environments.
  J Biosci Bioeng, 98, 317-330.  
15529406 J.B.Seo, H.S.Kim, G.Y.Jung, M.H.Nam, J.H.Chung, J.Y.Kim, J.S.Yoo, C.W.Kim, and O.Kwon (2004).
Psychrophilicity of Bacillus psychrosaccharolyticus: a proteomic study.
  Proteomics, 4, 3654-3659.  
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.