2VWS

Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure and Functional Assignment of Yfau, a Metal Ion Dependent Class II Aldolase from Escherichia Coli K12.

Rea, D.Hovington, R.Rakus, J.F.Gerlt, J.A.Fulop, V.Bugg, T.D.H.Roper, D.I.

(2008) Biochemistry 47: 9955

  • DOI: 10.1021/bi800943g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • One of the major challenges in the postgenomic era is the functional assignment of proteins using sequence- and structure-based predictive methods coupled with experimental validation. We have used these approaches to investigate the structure and fu ...

    One of the major challenges in the postgenomic era is the functional assignment of proteins using sequence- and structure-based predictive methods coupled with experimental validation. We have used these approaches to investigate the structure and function of the Escherichia coli K-12 protein YfaU, annotated as a putative 4-hydroxy-2-ketoheptane-1,7-dioate aldolase (HpcH) in the sequence databases. HpcH is the final enzyme in the degradation pathway of the aromatic compound homoprotocatechuate. We have determined the crystal structure of apo-YfaU and the Mg (2+)-pyruvate product complex. Despite greater sequence and structural similarity to HpcH, genomic context suggests YfaU is instead a 2-keto-3-deoxy sugar aldolase like the homologous 2-dehydro-3-deoxygalactarate aldolase (DDGA). Enzyme kinetic measurements show activity with the probable physiological substrate 2-keto-3-deoxy- l-rhamnonate, supporting the functional assignment, as well as the structurally similar 2-keto-3-deoxy- l-mannonate and 2-keto-3-deoxy- l-lyxonate (see accompanying paper: Rakus, J. F., Fedorov, A. A., Fedorov, E. V., Glasner, M. E., Hubbard, B. K., Delli, J. D., Babbitt, P. C., Almo, S. C., and Gerlt, J. A. (2008) Biochemistry 47, 9944-9954). YfaU has similar activity toward the HpcH substrate 4-hydroxy-2-ketoheptane-1,7-dioate and synthetic substrates 4-hydroxy-2-ketopentanoic acid and 4-hydroxy-2-ketohexanoic acid. This indicates a relaxed substrate specificity that complicates the functional assignment of members of this enzyme superfamily. Crystal structures suggest these enzymes use an Asp-His intersubunit dyad to activate a metal-bound water or hydroxide for proton transfer during catalysis.


    Organizational Affiliation

    Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
A, B, C
267Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rhmA (yfaU)
EC: 4.1.2.53
Find proteins for P76469 (Escherichia coli (strain K12))
Go to UniProtKB:  P76469
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 105.200α = 90.00
b = 136.800β = 90.00
c = 123.200γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance