3HYC

Crystal structure of E. coli phosphatase YrbI, with Mg, tetragonal form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

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This is version 1.1 of the entry. See complete history. 


Literature

The Tail of KdsC: CONFORMATIONAL CHANGES CONTROL THE ACTIVITY OF A HALOACID DEHALOGENASE SUPERFAMILY PHOSPHATASE.

Biswas, T., Yi, L., Aggarwal, P., Wu, J., Rubin, J.R., Stuckey, J.A., Woodard, R.W., Tsodikov, O.V.

(2009) J Biol Chem 284: 30594-30603

  • DOI: 10.1074/jbc.M109.012278
  • Primary Citation of Related Structures:  
    3I6B, 2R8E, 2R8Z, 2R8Y, 2R8X, 3HYC

  • PubMed Abstract: 

    • The phosphatase KdsC cleaves 3-deoxy-D-manno-octulosonate 8-phosphate to generate a molecule of inorganic phosphate and Kdo. Kdo is an essential component of the lipopolysaccharide envelope in Gram-negative bacteria. Because lipopolysaccharide is an impo ...

    The phosphatase KdsC cleaves 3-deoxy-D-manno-octulosonate 8-phosphate to generate a molecule of inorganic phosphate and Kdo. Kdo is an essential component of the lipopolysaccharide envelope in Gram-negative bacteria. Because lipopolysaccharide is an important determinant of bacterial resistance and toxicity, KdsC is a potential target for novel antibacterial agents. KdsC belongs to the broad haloacid dehalogenase superfamily. In haloacid dehalogenase superfamily enzymes, substrate specificity and catalytic efficiency are generally dictated by a fold feature called the cap domain. It is therefore not clear why KdsC, which lacks a cap domain, is catalytically efficient and highly specific to 3-deoxy-D-manno-octulosonate 8-phosphate. Here, we present a set of seven structures of tetrameric Escherichia coli KdsC (ranging from 1.4 to 3.06 A in resolution) that model different intermediate states in its catalytic mechanism. A crystal structure of product-bound E. coli KdsC shows how the interface between adjacent monomers defines the active site pocket. Kdo is engaged in a network of polar and nonpolar interactions with residues at this interface, which explains substrate specificity. Furthermore, this structural and kinetic analysis strongly suggests that the binding of the flexible C-terminal region (tail) to the active site makes KdsC catalytically efficient by facilitating product release.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase A, B, C, D, E, F, G, H188Escherichia coli BMutation(s): 0 
Gene Names: YrbI
EC: 3.1.3.45
Find proteins for P67653 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore P67653 
Go to UniProtKB:  P67653
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.219α = 90
b = 122.219β = 90
c = 202.173γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance