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PDBsum entry 3hpq

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protein ligands Protein-protein interface(s) links
Transferase PDB id
3hpq
Jmol
Contents
Protein chains
214 a.a. *
Ligands
AP5 ×2
Waters ×661
* Residue conservation analysis
PDB id:
3hpq
Name: Transferase
Title: Crystal structure of wild-type adenylate kinase from e. Coli complex with ap5a
Structure: Adenylate kinase. Chain: a, b. Synonym: ak, atp-amp transphosphorylase. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: adk, b0474, dnaw, jw0463, plsa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.204     R-free:   0.245
Authors: V.J.Hilser,T.P.Travis,D.W.Bolen
Key ref:
T.P.Schrank et al. (2009). Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins. Proc Natl Acad Sci U S A, 106, 16984-16989. PubMed id: 19805185 DOI: 10.1073/pnas.0906510106
Date:
04-Jun-09     Release date:   03-Nov-09    
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
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   2 terms 
  Biological process     AMP salvage   10 terms 
  Biochemical function     nucleotide binding     10 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0906510106 Proc Natl Acad Sci U S A 106:16984-16989 (2009)
PubMed id: 19805185  
 
 
Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins.
T.P.Schrank, D.W.Bolen, V.J.Hilser.
 
  ABSTRACT  
 
Elucidating the complex interplay between protein structure and dynamics is a prerequisite to an understanding of both function and adaptation in proteins. Unfortunately, it has been difficult to experimentally decouple these effects because it is challenging to rationally design mutations that will either affect the structure but not the dynamics, or that will affect the dynamics but not the structure. Here we adopt a mutation approach that is based on a thermal adaptation strategy observed in nature, and we use it to study the binding interaction of Escherichia coli adenylate kinase (AK). We rationally design several single-site, surface-exposed glycine mutations to selectively perturb the excited state conformational repertoire, leaving the ground-state X-ray crystallographic structure unaffected. The results not only demonstrate that the conformational ensemble of AK is significantly populated by a locally unfolded state that is depopulated upon binding, but also that the excited-state conformational ensemble can be manipulated through mutation, independent of perturbations of the ground-state structures. The implications of these results are twofold. First, they indicate that it is possible to rationally design dynamic allosteric mutations, which do not propagate through a pathway of structural distortions connecting the mutated and the functional sites. Secondly and equally as important, the results reveal a general strategy for thermal adaptation that allows enzymes to modulate binding affinity by controlling the amount of local unfolding in the native-state ensemble. These findings open new avenues for rational protein design and fundamentally illuminate the role of local unfolding in function and adaptation.
 
  Selected figure(s)  
 
Figure 1.
Mutation strategy applied to adenylate kinase. Structure of “Open” [i.e., Apo-AK; (PDB ID 4AKE) (11)] and “Closed” [i.e., complex of AK and the nonhydrolysable bisubstrate analogue inhibitor P^1,P^5-Di(adenosine) pentaphosphate (Ap5A); PDB ID 1AKE (10)] states of AK. LID is shown in gray. The “LID domain,” as defined by Shapiro et al. (7). AMPbd is shown in green. The “AMP binding domain” (7). Red spheres, selected mutation sites.
Figure 4.
Surface Gly mutations in LID conserve ground-state structure. (A) Alignment of the reported crystal structures of WT and v148g AK. Shown in red are chains (WT and v148g) from position A within the asymmetric unit. Shown in black are chains from position B within the asymmetric unit. (B) ^1H-^15N HSQC spectra of WT (black) and v142g (red) AK at 21° C, which suppress local unfolding within the LID region. Enhanced contrast is used for v142g to allow visualization of peaks with decreased intensity, most likely because of exchange broadening. Available assignments are provided for resonances with differences at this temperature. (C) Analysis of structural perturbations effected by mutation. The gray spheres represent all atoms that move >0.3 Å from the WT to mutant structure in both copies within the ASU. The dark red spheres show the mutation site (position 148). The light red spheres show all perturbed atoms (gray) that can be connected to the mutation site by a continuous chain (< 6 Å per step) of other perturbed atoms. Blue spheres, Ap5A.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21404360 C.G.Kalodimos (2011).
NMR reveals novel mechanisms of protein activity regulation.
  Protein Sci, 20, 773-782.  
  21365689 D.Armenta-Medina, E.Pérez-Rueda, and L.Segovia (2011).
Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches.
  Proteins, 79, 1662-1671.  
21157775 R.J.Falconer, and B.M.Collins (2011).
Survey of the year 2009: applications of isothermal titration calorimetry.
  J Mol Recognit, 24, 1.  
21307307 W.Li, P.G.Wolynes, and S.Takada (2011).
Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins.
  Proc Natl Acad Sci U S A, 108, 3504-3509.  
21081091 J.B.Brokaw, and J.W.Chu (2010).
On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase.
  Biophys J, 99, 3420-3429.  
20361049 J.O.Wrabl, and V.J.Hilser (2010).
Investigating homology between proteins using energetic profiles.
  PLoS Comput Biol, 6, e1000722.  
20541943 P.Csermely, R.Palotai, and R.Nussinov (2010).
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events.
  Trends Biochem Sci, 35, 539-546.  
21081909 U.Olsson, and M.Wolf-Watz (2010).
Overlap between folding and functional energy landscapes for adenylate kinase conformational change.
  Nat Commun, 1, 111.  
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.