1E4Y

Mutant P9L of adenylate kinase from E. coli, modified in the Gly-loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop.

Muller, C.W.Schulz, G.E.

(1993) Proteins 15: 42-49

  • DOI: 10.1002/prot.340150106
  • Primary Citation of Related Structures:  
    1E4V, 1E4Y

  • PubMed Abstract: 
  • Two mutants of adenylate kinase from Escherichia coli have been crystallized and analyzed by X-ray diffraction at resolutions of 3.4 and 2.4 A, respectively. These mutants are Pro-9-->Leu and Gly-10-->Val. They were selected for their positions in th ...

    Two mutants of adenylate kinase from Escherichia coli have been crystallized and analyzed by X-ray diffraction at resolutions of 3.4 and 2.4 A, respectively. These mutants are Pro-9-->Leu and Gly-10-->Val. They were selected for their positions in the highly conserved Gly-loop forming a giant anion hole for the beta-phosphate of ATP (GTP) in adenylate kinases, H-ras-p21, and other nucleotide-binding proteins. Mutants at these positions of H-ras-p21 cause cancer. In adenylate kinase these mutations cause smallish changes at the active site. Relating the structural changes to the known changes in catalysis indicates that these mutants hinder the induced-fit movements. As a side result we find that mutant Pro-9-->Leu and wild-type form one very similar crystal packing contact that is crystallographic in one case and noncrystallographic in the other, while all other packing contacts and the space groups are quite at variance.


    Related Citations: 
    • Induced-Fit Movements in Adenylate Kinases
      Schulz, G.E., Mueller, C.W., Diederichs, K.
      (1990) J Mol Biol 213: 627
    • Structure of the Complex of Adenylate Kinase from Escherichia Coli with the Inhibitor P1, P5-Bis (Adenosine-5'-) Pentaphosphate
      Mueller, C.W., Schulz, G.E.
      (1988) J Mol Biol 202: 909

    Organizational Affiliation

    Institut für Organische Chemie und Biochemie der Universität, Freiburg im Breisgau, Federal Republic of Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenylate kinaseAB214Escherichia coliMutation(s): 1 
Gene Names: adkdnaWplsAb0474JW0463
EC: 2.7.4.3
Find proteins for P69441 (Escherichia coli (strain K12))
Explore P69441 
Go to UniProtKB:  P69441
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AP5
Query on AP5

Download CCD File 
A, B
BIS(ADENOSINE)-5'-PENTAPHOSPHATE
C20 H29 N10 O22 P5
OIMACDRJUANHTJ-XPWFQUROSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.3α = 90
b = 77.8β = 94.3
c = 57.7γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2018-11-21
    Changes: Data collection, Database references, Source and taxonomy, Structure summary