Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 128.26 kDa 
• Atom Count: 9148 
• Residue Count: 1041 
• Unique protein chains: 1

6OFU

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

• DOI: 10.2210/pdb6OFU/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-01 Released: 2019-04-24 
• Deposition Author(s): Dopkins, B.J., Thoden, J.B., Huddleston, J.P., Narindoshvili, T., Fose, B., Rachel, F.M., Holden, H.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Robert A. Welch Foundation

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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 

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

• PubMed: 31322866 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YdjI aldolase	A, B, C, D	286	Escherichia coli K-12	Mutation(s): 0  Gene Names: ydjI, b1773, JW1762
Find proteins for P77704 (Escherichia coli (strain K12)) Explore P77704  Go to UniProtKB:  P77704

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B, C, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A,B,C,D	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

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 = 80.763	α = 90
b = 85.663	β = 109.88
c = 84.268	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-04-01 
• Released Date: 2019-04-24 
Deposition Author(s): Dopkins, B.J., Thoden, J.B., Huddleston, J.P., Narindoshvili, T., Fose, B., Rachel, F.M., Holden, H.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM122825
Robert A. Welch Foundation	United States	A-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