8BLM

Structure of RutB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.266 

Starting Model: in silico
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This is version 1.4 of the entry. See complete history


Literature

Structural and Functional Characterization of the Ureidoacrylate Amidohydrolase RutB from Escherichia coli .

Busch, M.R.Rajendran, C.Sterner, R.

(2023) Biochemistry 62: 863-872

  • DOI: https://doi.org/10.1021/acs.biochem.2c00640
  • Primary Citation of Related Structures:  
    8BKD, 8BLL, 8BLM, 8BLN, 8BYW

  • PubMed Abstract: 

    We present a detailed structure-function analysis of the ureidoacrylate amidohydrolase RutB from Eschericha coli , which is an essential enzyme of the Rut pathway for pyrimidine utilization. Crystals of selenomethionine-labeled RutB were produced, which allowed us to determine the first structure of the enzyme at a resolution of 1.9 Å and to identify it as a new member of the isochorismatase-like hydrolase family. RutB was co-crystallized with the substrate analogue ureidopropionate, revealing the mode of substrate binding. Mutation of residues constituting the catalytic triad (D24A, D24N, K133A, C166A, C166S, C166T, C166Y) resulted in complete inactivation of RutB, whereas mutation of other residues close to the active site (Y29F, Y35F, N72A, W74A, W74F, E80A, E80D, S92A, S92T, S92Y, Q105A, Y136A, Y136F) leads to distinct changes of the turnover number ( k cat ) and/or the Michaelis constant ( K M ). The results of our structural and mutational studies allowed us to assign specific functions to individual residues and to formulate a plausible reaction mechanism for RutB.


  • Organizational Affiliation

    Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ureidoacrylate amidohydrolase RutB
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
230Escherichia coli K-12Mutation(s): 0 
Gene Names: rutBEcDH1_2631ECDH1ME8569_0965
EC: 3.5.1.110
UniProt
Find proteins for P75897 (Escherichia coli (strain K12))
Explore P75897 
Go to UniProtKB:  P75897
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75897
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.266 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.592α = 90
b = 110.89β = 99.13
c = 128.714γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-10-11
    Changes: Refinement description
  • Version 1.4: 2023-11-15
    Changes: Source and taxonomy