5WAS

Corynebacterium glutamicum Hydrolyzed Homoserine kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Reduction of Feedback Inhibition in Homoserine Kinase (ThrB) ofCorynebacterium glutamicumEnhances l-Threonine Biosynthesis.

Petit, C.Kim, Y.Lee, S.K.Brown, J.Larsen, E.Ronning, D.R.Suh, J.W.Kang, C.M.

(2018) ACS Omega 3: 1178-1186

  • DOI: https://doi.org/10.1021/acsomega.7b01597
  • Primary Citation of Related Structures:  
    5WAS, 5WAT

  • PubMed Abstract: 

    l-Threonine is an important supplement in the food industry. It is currently produced through fermentation of Escherichia coli but requires additional purification steps to remove E. coli endotoxin. To avoid these steps, it is desirable to use Corynebacterium glutamicum , a microorganism generally regarded as safe. Engineering of C. glutamicum to increase production of l-threonine has mainly focused on gene regulation as well as l-threonine export or carbon flux depletion. In this study, we focus on the negative feedback inhibition produced by l-threonine on the enzyme homoserine kinase (ThrB). Although l-threonine binds to allosteric sites of aspartate kinase (LysC) and homoserine dehydrogenase (Hom), serving as a noncompetitive inhibitor, it acts as a competitive inhibitor on ThrB. This is problematic when attempting to engineer enzymes that are nonresponsive to increasing cellular concentrations of l-threonine. Using primary structure alignment as well as analysis of the Methanocaldococcus jannaschii ThrB ( Mja ThrB) active site in complex with l-threonine (inhibitor of ThrB) and l-homoserine (substrate of ThrB), a conserved active-site alanine residue (A20) in C. glutamicum ThrB ( Cgl ThrB) was predicted to be important for differential interactions with l-threonine and l-homoserine. Through site-directed mutagenesis, we show that one variant of C. glutamicum ThrB, Cgl ThrB-A20G, retains wild-type enzymatic activity, with dramatically decreased feedback inhibition by l-threonine. Additionally, by solving the first Corynebacterium X-ray crystal structure of homoserine kinase, we can confirm that the changes in l-threonine affinity to the Cgl ThrB-A20G active site derive from loss of van der Waals interactions.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Toledo, 2801 W. Bancroft Street, Toledo, Ohio 43606, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homoserine kinase185Corynebacterium glutamicumMutation(s): 0 
Gene Names: thrBCgl1184cg1338
EC: 2.7.1.39
UniProt
Find proteins for P07128 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore P07128 
Go to UniProtKB:  P07128
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07128
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Homoserine kinase55Corynebacterium glutamicumMutation(s): 0 
Gene Names: thrBCgl1184cg1338
EC: 2.7.1.39
UniProt
Find proteins for P07128 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore P07128 
Go to UniProtKB:  P07128
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07128
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Homoserine kinase75Corynebacterium glutamicumMutation(s): 0 
Gene Names: thrBCgl1184cg1338
EC: 2.7.1.39
UniProt
Find proteins for P07128 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore P07128 
Go to UniProtKB:  P07128
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07128
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.245 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.227α = 90
b = 46.227β = 90
c = 267.295γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description