Crystal structure of E. coli glucokinase in complex with glucose

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


Crystal structures of Escherichia coli ATP-dependent glucokinase and its complex with glucose

Lunin, V.V.Li, Y.Schrag, J.D.Iannuzzi, P.Cygler, M.Matte, A.

(2004) J Bacteriol 186: 6915-6927

  • DOI: https://doi.org/10.1128/JB.186.20.6915-6927.2004
  • Primary Citation of Related Structures:  
    1Q18, 1SZ2

  • PubMed Abstract: 

    Intracellular glucose in Escherichia coli cells imported by phosphoenolpyruvate-dependent phosphotransferase system-independent uptake is phosphorylated by glucokinase by using ATP to yield glucose-6-phosphate. Glucokinases (EC are functionally distinct from hexokinases (EC with respect to their narrow specificity for glucose as a substrate. While structural information is available for ADP-dependent glucokinases from Archaea, no structural information exists for the large sequence family of eubacterial ATP-dependent glucokinases. Here we report the first structure determination of a microbial ATP-dependent glucokinase, that from E. coli O157:H7. The crystal structure of E. coli glucokinase has been determined to a 2.3-A resolution (apo form) and refined to final Rwork/Rfree factors of 0.200/0.271 and to 2.2-A resolution (glucose complex) with final Rwork/Rfree factors of 0.193/0.265. E. coli GlK is a homodimer of 321 amino acid residues. Each monomer folds into two domains, a small alpha/beta domain (residues 2 to 110 and 301 to 321) and a larger alpha+beta domain (residues 111 to 300). The active site is situated in a deep cleft between the two domains. E. coli GlK is structurally similar to Saccharomyces cerevisiae hexokinase and human brain hexokinase I but is distinct from the ADP-dependent GlKs. Bound glucose forms hydrogen bonds with the residues Asn99, Asp100, Glu157, His160, and Glu187, all of which, except His160, are structurally conserved in human hexokinase 1. Glucose binding results in a closure of the small domains, with a maximal Calpha shift of approximately 10 A. A catalytic mechanism is proposed that is consistent with Asp100 functioning as the general base, abstracting a proton from the O6 hydroxyl of glucose, followed by nucleophilic attack at the gamma-phosphoryl group of ATP, yielding glucose-6-phosphate as the product.

  • Organizational Affiliation

    Biotechnology Research Institute, NRCC, 6100 Royalmount Ave., Montreal, Quebec H4P 2R2 Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
332Escherichia coliMutation(s): 6 
Gene Names: GLKB2388Z3654ECS3268
Find proteins for P0A6V9 (Escherichia coli O157:H7)
Explore P0A6V9 
Go to UniProtKB:  P0A6V9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6V9
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.416α = 90
b = 53.538β = 112.99
c = 90.903γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2023-11-15
    Changes: Data collection