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PDBsum entry 2rgx

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protein ligands metals links
Transferase PDB id
2rgx
Jmol
Contents
Protein chain
203 a.a. *
Ligands
AP5
Metals
_ZN ×4
Waters ×113
* Residue conservation analysis
PDB id:
2rgx
Name: Transferase
Title: Crystal structure of adenylate kinase from aquifex aeolicus with ap5a
Structure: Adenylate kinase. Chain: a. Synonym: atp-amp transphosphorylase. Engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Gene: adk. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.209     R-free:   0.243
Authors: V.Thai,M.Wolf-Watz,T Fenn,E.Pozharski,M.A.Wilson,G.A.Petsko,
Key ref:
K.A.Henzler-Wildman et al. (2007). Intrinsic motions along an enzymatic reaction trajectory. Nature, 450, 838-844. PubMed id: 18026086 DOI: 10.1038/nature06410
Date:
05-Oct-07     Release date:   18-Dec-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O66490  (KAD_AQUAE) -  Adenylate kinase
Seq:
Struc:
206 a.a.
203 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 54.39% 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     AMP salvage   5 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nature06410 Nature 450:838-844 (2007)
PubMed id: 18026086  
 
 
Intrinsic motions along an enzymatic reaction trajectory.
K.A.Henzler-Wildman, V.Thai, M.Lei, M.Ott, M.Wolf-Watz, T.Fenn, E.Pozharski, M.A.Wilson, G.A.Petsko, M.Karplus, C.G.Hübner, D.Kern.
 
  ABSTRACT  
 
The mechanisms by which enzymes achieve extraordinary rate acceleration and specificity have long been of key interest in biochemistry. It is generally recognized that substrate binding coupled to conformational changes of the substrate-enzyme complex aligns the reactive groups in an optimal environment for efficient chemistry. Although chemical mechanisms have been elucidated for many enzymes, the question of how enzymes achieve the catalytically competent state has only recently become approachable by experiment and computation. Here we show crystallographic evidence for conformational substates along the trajectory towards the catalytically competent 'closed' state in the ligand-free form of the enzyme adenylate kinase. Molecular dynamics simulations indicate that these partially closed conformations are sampled in nanoseconds, whereas nuclear magnetic resonance and single-molecule fluorescence resonance energy transfer reveal rare sampling of a fully closed conformation occurring on the microsecond-to-millisecond timescale. Thus, the larger-scale motions in substrate-free adenylate kinase are not random, but preferentially follow the pathways that create the configuration capable of proficient chemistry. Such preferred directionality, encoded in the fold, may contribute to catalysis in many enzymes.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Kinetic model and X-ray structure of Aquifex Adk. a, Proposed reaction scheme for the enzyme adenylate kinase (E) including the steps of substrate binding (k[on]), lid closing (k[close]), phospho-transfer (k[p-transfer]), lid opening (k[open]) and substrate dissociation (k[off]). b, Superposition of molecule A (for definition, see Fig. 2) of apo Aquifex (red) with apo E. coli (blue) Adk reveals only small changes in the overall structure between the homologues, as indicated by dashed ovals. c, Superposition of apo Aquifex Adk (red) and Aquifex Adk in complex (green) with the substrate analogue Zn^2+ Ap5A (shown as ball and stick in grey) demonstrates the closure of the ATP and AMP lids on substrate binding.
Figure 2.
Figure 2: Conformational substates of ligand-free Aquifex Adk detected in the crystal structure. a, Superposition of the three molecules, A, B and C, in the asymmetric unit of apo Adk (red, orange and yellow, respectively) and Adk complexed with Zn^2+ Ap5A (green; Zn^2+ from the crystallization mother liquor is bound to the Mg^2+ site). The substates A, B and C lie along the reaction trajectory towards the closed state. b, Backbone displacement of A (red), B (orange) and C (yellow) relative to the inhibitor-bound form. c, d, The conformational substates A, B and C are a result of motions around eight hinges, indicated by arrows (for details about the hinges, see ref. 22). For better visualization of the hinges of the ATP lid, the latter was rotated by 90° (d) with respect to a. The two views in c show the AMP lid with different segments overlaid to highlight the two distinct hinge pairs. e, 2F[o]–F[c] maps contoured at 1.0 of the ATP lids of molecules A (left), B (centre) and C (right) show the quality of the electron density.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 450, 838-844) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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PDB codes: 2xb4 3l0p 3l0s
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Biochemistry. Reengineering enzymes.
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Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase.
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PDB codes: 3a3w 3a3x 3a4j
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Approximate reconstruction of continuous spatially complex domain motions by multialignment NMR residual dipolar couplings.
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Data-driven approach to decomposing complex enzyme kinetics with surrogate models.
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A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.
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PDB code: 2kn5
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PDB codes: 2k0e 2k0f
18678900 K.Okazaki, and S.Takada (2008).
Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms.
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18682219 M.B.Kubitzki, and B.L.de Groot (2008).
The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study.
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18941632 M.Cardó-Vila, A.J.Zurita, R.J.Giordano, J.Sun, R.Rangel, L.Guzman-Rojas, C.D.Anobom, A.P.Valente, F.C.Almeida, J.Lahdenranta, M.G.Kolonin, W.Arap, and R.Pasqualini (2008).
A ligand peptide motif selected from a cancer patient is a receptor-interacting site within human interleukin-11.
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18704171 M.Cecchini, A.Houdusse, and M.Karplus (2008).
Allosteric communication in myosin V: from small conformational changes to large directed movements.
  PLoS Comput Biol, 4, e1000129.  
18412261 M.S.Liu, B.D.Todd, S.Yao, Z.P.Feng, R.S.Norton, and R.J.Sadus (2008).
Coarse-grained dynamics of the receiver domain of NtrC: fluctuations, correlations and implications for allosteric cooperativity.
  Proteins, 73, 218-227.  
18676657 N.Kantarci-Carsibasi, T.Haliloglu, and P.Doruker (2008).
Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes.
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19404472 P.C.Whitford, J.N.Onuchic, and P.G.Wolynes (2008).
Energy landscape along an enzymatic reaction trajectory: hinges or cracks?
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18840689 R.K.Eppler, E.P.Hudson, S.D.Chase, J.S.Dordick, J.A.Reimer, and D.S.Clark (2008).
Biocatalyst activity in nonaqueous environments correlates with centisecond-range protein motions.
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18946041 S.Saen-Oon, S.Quaytman-Machleder, V.L.Schramm, and S.D.Schwartz (2008).
Atomic detail of chemical transformation at the transition state of an enzymatic reaction.
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Dynamic personalities of proteins.
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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.