6Z9I

Escherichia coli D-2-deoxyribose-5-phosphate aldolase - N21K mutant complex with reaction products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods.

Voutilainen, S.Heinonen, M.Andberg, M.Jokinen, E.Maaheimo, H.Paakkonen, J.Hakulinen, N.Rouvinen, J.Lahdesmaki, H.Kaski, S.Rousu, J.Penttila, M.Koivula, A.

(2020) Appl Microbiol Biotechnol 104: 10515-10529

  • DOI: 10.1007/s00253-020-10960-x
  • Primary Citation of Related Structures:  
    6Z9H, 6Z9J, 6Z9I

  • PubMed Abstract: 
  • In this work, deoxyribose-5-phosphate aldolase (Ec DERA, EC 4.1.2.4) from Escherichia coli was chosen as the protein engineering target for improving the substrate preference towards smaller, non-phosphorylated aldehyde donor substrates, in particula ...

    In this work, deoxyribose-5-phosphate aldolase (Ec DERA, EC 4.1.2.4) from Escherichia coli was chosen as the protein engineering target for improving the substrate preference towards smaller, non-phosphorylated aldehyde donor substrates, in particular towards acetaldehyde. The initial broad set of mutations was directed to 24 amino acid positions in the active site or in the close vicinity, based on the 3D complex structure of the E. coli DERA wild-type aldolase. The specific activity of the DERA variants containing one to three amino acid mutations was characterised using three different substrates. A novel machine learning (ML) model utilising Gaussian processes and feature learning was applied for the 3rd mutagenesis round to predict new beneficial mutant combinations. This led to the most clear-cut (two- to threefold) improvement in acetaldehyde (C2) addition capability with the concomitant abolishment of the activity towards the natural donor molecule glyceraldehyde-3-phosphate (C3P) as well as the non-phosphorylated equivalent (C3). The Ec DERA variants were also tested on aldol reaction utilising formaldehyde (C1) as the donor. Ec DERA wild-type was shown to be able to carry out this reaction, and furthermore, some of the improved variants on acetaldehyde addition reaction turned out to have also improved activity on formaldehyde. KEY POINTS: • DERA aldolases are promiscuous enzymes. • Synthetic utility of DERA aldolase was improved by protein engineering approaches. • Machine learning methods aid the protein engineering of DERA.


    Organizational Affiliation

    VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyribose-phosphate aldolaseAB250Escherichia coliMutation(s): 1 
Gene Names: 
deoCA6592_04055A9819_24930AJ318_04090AML35_20375AWE53_009755AWF59_004780AWG90_001355AZZ83_003140B9M99_13055BHF46_08905BIU72_19175BIZ41_21315BK292_12675BK296_03525BK375_05655BON91_08010BvCmsC61A_04176BvCmsHHP001_01002BvCmsKKP061_00143BvCmsKSP045_01273BvCmsKSP067_04018BvCmsKSP076_01350BvCmsNSP047_00091BvCmsSINP022_00140BZL69_04490C4M78_04295C7B08_10715C7B18_26170CDC27_23655D2188_24830D3P01_08005D9D31_02570D9E34_05115D9G48_24275D9I87_14825D9I88_23755D9K54_15785DD762_00045DND16_14490DNQ45_13620DTL90_19480DTM45_25725DU321_02660DXT71_19415E0L12_12025E5S46_05005E5S58_22595E5S61_04910EC382_07685EL79_3891EL80_3836ELT23_13160ELV08_18870ELV15_04550ELV28_15080EQ825_04285EQ830_02895ERS085386_00787EVY14_13465EXX13_04350EXX23_12990EXX53_09895EYY34_19360FNJ83_01355FV438_05665FWK02_17600FY127_22350HMPREF3040_02396NCTC10090_02419NCTC7922_05561NCTC9117_05294NCTC9777_00681NCTC9969_04462PGD_03624SAMEA3472056_01168SAMEA3472108_04807SAMEA3485101_00909SAMEA3485113_03629SAMEA3752559_04076SAMEA3753300_03100UC41_15640D3P02_09120D9E73_03455D9J52_08640D9J58_21915DL251_08360E4A44_15160E4K51_15620E5S62_07330EA174_02765EA200_11925EA218_06115EA233_02710EA235_11540EA242_12740EA245_11525EA433_11895ED307_16090ELT17_00260ELY41_04215FPI65_27080FQ021_21655GFU40_17080GFU47_22655GHR40_01535GIJ01_04545GIY13_03560GKE15_06175GKE16_06165GKE22_03160GKE24_07235GKE26_06175GKE29_09775GKE31_06140GKE39_04905GKE46_03185GKE53_03185GKE58_06095GKE60_06150GKE64_03185GKE69_04490GKE77_06520GKE79_04895GKE87_06015GKE92_02965GKE93_17900GKE98_07890GKF00_11475GKF03_01395GNZ00_05540GP720_10555GQM13_11645GRW27_14885GRW57_19405GUB08_06635GUC40_07220GUI16_07100HmCmsJML236_01698NCTC12650_04544NCTC9001_05155

EC: 4.1.2.4
Find proteins for E2QLE1 (Escherichia coli)
Explore E2QLE1 
Go to UniProtKB:  E2QLE1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G3H
Query on G3H

Download CCD File 
B
GLYCERALDEHYDE-3-PHOSPHATE
C3 H7 O6 P
LXJXRIRHZLFYRP-VKHMYHEASA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.9α = 90
b = 53.3β = 110.2
c = 81.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland288677

Revision History 

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references