8BLL

Structure of RutB

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1021/acs.biochem.2c00640
  • Primary Citation of Related Structures:  
    8BKD, 8BLL, 8BLM, 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ureidoacrylate amidohydrolase RutB
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
230Escherichia coliMutation(s): 0 
Gene Names: rutB, EcDH1_2631, ECDH1ME8569_0965
EC: 3.5.1.110
UniProt
Find proteins for C9QZ65 (Escherichia coli (strain ATCC 33849 / DSM 4235 / NCIMB 12045 / K12 / DH1))
Explore C9QZ65 
Go to UniProtKB:  C9QZ65
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC9QZ65
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT (Subject of Investigation/LOI)
Query on ACT
Download Ideal Coordinates CCD File 
AA [auth F],
BA [auth F],
CA [auth G],
DA [auth G],
EA [auth H],
AA [auth F],
BA [auth F],
CA [auth G],
DA [auth G],
EA [auth H],
FA [auth H],
GA [auth I],
HA [auth I],
IA [auth J],
JA [auth J],
KA [auth K],
LA [auth K],
MA [auth L],
NA [auth L],
OA [auth M],
PA [auth M],
Q [auth A],
QA [auth N],
R [auth A],
RA [auth N],
S [auth B],
SA [auth O],
T [auth B],
TA [auth O],
U [auth C],
UA [auth P],
V [auth C],
VA [auth P],
W [auth D],
X [auth D],
Y [auth E],
Z [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.456α = 85.66
b = 108.609β = 83.22
c = 124.341γ = 74.34
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