1E4V

Mutant G10V of adenylate kinase from E. coli, modified in the Gly-loop

• PDB DOI: https://doi.org/10.2210/pdb1E4V/pdb

• Classification: TRANSFERASE(PHOSPHOTRANSFERASE)
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-07-12 Released: 2000-08-04 
• Deposition Author(s): Mueller, C.W., Schulz, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

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

• PubMed: 8451239 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 49.16 kDa 
• Atom Count: 3,780 
• Modelled Residue Count: 428 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B	214	Escherichia coli	Mutation(s): 1  Gene Names: adk, dnaW, plsA, b0474, JW0463 EC: 2.7.4.3
UniProt
Find proteins for P69441 (Escherichia coli (strain K12)) Explore P69441  Go to UniProtKB:  P69441

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AP5	C [auth A], D [auth B]	BIS(ADENOSINE)-5'-PENTAPHOSPHATE C20 H29 N10 O22 P5 OIMACDRJUANHTJ-XPWFQUROSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.2	α = 90
b = 79.8	β = 90
c = 85	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-08-04 
Deposition Author(s): Mueller, C.W., Schulz, G.E.

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: 2018-09-19
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.5: 2024-05-08
  Changes: Data collection, Database references, Derived calculations