6OFU image
Entry Detail
PDB ID:
6OFU
Keywords:
Title:
X-ray crystal structure of the YdjI aldolase from Escherichia coli K12
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2019-04-01
Release Date:
2019-04-24
Method Details:
Experimental Method:
Resolution:
1.75 Å
R-Value Free:
0.18
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:YdjI aldolase
Chain IDs:A, B, C, D
Chain Length:286
Number of Molecules:4
Biological Source:Escherichia coli (strain K12)
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
OCS A CYS modified residue
Primary Citation
Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity inEscherichia coliK12.
Biochemistry 58 3340 3353 (2019)
PMID: 31322866 DOI: 10.1021/acs.biochem.9b00326

Abstact

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 kcat of 3.0 s-1. The product, l-glycero-l-galacto-octuluronate-1-phosphate, has a kcat/Km value of 2.1 × 103 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.

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