2JGR

Crystal structure of YegS in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb2JGR/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli BL21
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-02-14 Released: 2007-05-15 
• Deposition Author(s): Bakali, H.M., Herman, M.D., Johnson, K.A., Kelly, A.A., Wieslander, A., Hallberg, B.M., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.249 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Starting Model: experimental

Literature

Crystal Structure of Yegs, a Homologue to the Mammalian Diacylglycerol Kinases, Reveals a Novel Regulatory Metal Binding Site.

Bakali, H.M., Herman, M.D., Johnson, K.A., Kelly, A.A., Wieslander, A., Hallberg, B.M., Nordlund, P.

(2007) J Biol Chem 282: 19644

• PubMed: 17351295 
• DOI: https://doi.org/10.1074/jbc.M604852200
• Primary Citation of Related Structures:  
  2BON, 2JGR


• PubMed Abstract: 
  

  The human lipid kinase family controls cell proliferation, differentiation, and tumorigenesis and includes diacylglycerol kinases, sphingosine kinases, and ceramide kinases. YegS is an Escherichia coli protein with significant sequence homology to the catalytic domain of the human lipid kinases. We have solved the crystal structure of YegS and shown that it is a lipid kinase with phosphatidylglycerol kinase activity. The crystal structure reveals a two-domain protein with significant structural similarity to a family of NAD kinases. The active site is located in the interdomain cleft formed by four conserved sequence motifs. Surprisingly, the structure reveals a novel metal binding site composed of residues conserved in most lipid kinases.

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Organizational Affiliation: 

Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 32.57 kDa 
• Atom Count: 2,001 
• Modelled Residue Count: 261 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YEGS	A	299	Escherichia coli BL21	Mutation(s): 0  EC: 2.7.1
UniProt
Find proteins for P76407 (Escherichia coli (strain K12)) Explore P76407  Go to UniProtKB:  P76407

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POP	B [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.249 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.968	α = 90
b = 124.968	β = 90
c = 54.163	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Bakali, H.M., Herman, M.D., Johnson, K.A., Kelly, A.A., Wieslander, A., Hallberg, B.M., Nordlund, P.

Revision History  

• Version 1.0: 2007-05-15
  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: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary