4ZXZ

Crystal structure of a highly thermal stable but inactive levoglucosan kinase.

• PDB DOI: https://doi.org/10.2210/pdb4ZXZ/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Lipomyces starkeyi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-20 Released: 2015-09-23 
• Deposition Author(s): Bacik, J.P., Klesmith, J.R., Whitehead, T.A.
• Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli.

Klesmith, J.R., Bacik, J.P., Michalczyk, R., Whitehead, T.A.

(2015) ACS Synth Biol 4: 1235-1243

• PubMed: 26369947 
• DOI: https://doi.org/10.1021/acssynbio.5b00131
• Primary Citation of Related Structures:  
  4ZXZ


• PubMed Abstract: 
  

  Synthetic metabolic pathways often suffer from low specific productivity, and new methods that quickly assess pathway functionality for many thousands of variants are urgently needed. Here we present an approach that enables the rapid and parallel determination of sequence effects on flux for complete gene-encoding sequences. We show that this method can be used to determine the effects of over 8000 single point mutants of a pyrolysis oil catabolic pathway implanted in Escherichia coli. Experimental sequence-function data sets predicted whether fitness-enhancing mutations to the enzyme levoglucosan kinase resulted from enhanced catalytic efficiency or enzyme stability. A structure of one design incorporating 38 mutations elucidated the structural basis of high fitness mutations. One design incorporating 15 beneficial mutations supported a 15-fold improvement in growth rate and greater than 24-fold improvement in enzyme activity relative to the starting pathway. This technique can be extended to improve a wide variety of designed pathways.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 98.92 kDa 
• Atom Count: 7,034 
• Modelled Residue Count: 862 
• Deposited Residue Count: 894 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Levoglucosan kinase	A, B	447	Lipomyces starkeyi	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.18	α = 90
b = 88.95	β = 90
c = 139.46	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-23 
Deposition Author(s): Bacik, J.P., Klesmith, J.R., Whitehead, T.A.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1254238
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 1.1: 2015-09-30
  Changes: Database references
• Version 1.2: 2015-12-02
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.4: 2019-11-27
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description