6OFU

X-ray crystal structure of the YdjI aldolase from Escherichia coli K12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity inEscherichia coliK12.

Huddleston, J.P.Thoden, J.B.Dopkins, B.J.Narindoshvili, T.Fose, B.J.Holden, H.M.Raushel, F.M.

(2019) Biochemistry 58: 3340-3353

  • DOI: 10.1021/acs.biochem.9b00326
  • Primary Citation of Related Structures:  
    6OFU

  • PubMed Abstract: 
  • The ydj gene cluster is found in 80% of sequenced Escherichia coli genomes and other closely related species in the human microbiome. On the basis of the annotations of the enzymes located in this cluster, it is expected that together t ...

    The ydj gene cluster is found in 80% of sequenced Escherichia coli genomes and other closely related species in the human microbiome. On the basis of the annotations of the enzymes located in this cluster, it is expected that together they catalyze the catabolism of an unknown carbohydrate. The focus of this investigation is on YdjI, which is in the ydj gene cluster of E. coli K-12. It is predicted to be a class II aldolase of unknown function. Here we describe a structural and functional characterization of this enzyme. YdjI catalyzes the hydrogen/deuterium exchange of the pro- S hydrogen at C3 of dihydroxyacetone phosphate (DHAP). In the presence of DHAP, YdjI catalyzes an aldol condensation with a variety of aldo sugars. YdjI shows a strong preference for higher-order (seven-, eight-, and nine-carbon) monosaccharides with specific hydroxyl stereochemistries and a negatively charged terminus (carboxylate or phosphate). The best substrate is l-arabinuronic acid with an apparent k cat of 3.0 s -1 . The product, l- glycero -l- galacto -octuluronate-1-phosphate, has a k cat / K m value of 2.1 × 10 3 M -1 s -1 in the retro-aldol reaction with YdjI. This is the first recorded synthesis of l- glycero -l- galacto -octuluronate-1-phosphate and six similar carbohydrates. The crystal structure of YdjI, determined to a nominal resolution of 1.75 Å (Protein Data Bank entry 6OFU ), reveals unusual positions for two arginine residues located near the active site. Computational docking was utilized to distinguish preferable binding orientations for l- glycero -l- galacto -octuluronate-1-phosphate. These results indicate a possible alternative binding orientation for l- glycero -l- galacto -octuluronate-1-phosphate compared to that observed in other class II aldolases, which utilize shorter carbohydrate molecules.


    Organizational Affiliation

    Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YdjI aldolase ABCD286Escherichia coli K-12Mutation(s): 0 
Gene Names: ydjIb1773JW1762
Find proteins for P77704 (Escherichia coli (strain K12))
Explore P77704 
Go to UniProtKB:  P77704
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A,B,C,DL-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.763α = 90
b = 85.663β = 109.88
c = 84.268γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122825
Robert A. Welch FoundationUnited StatesA-840

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence