Crystal structure of B. fragilis N-succinylornithine transcarbamylase P90E mutant complexed with carbamoyl phosphate and N-acetylnorvaline

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

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This is version 1.5 of the entry. See complete history


A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase.

Shi, D.Yu, X.Cabrera-Luque, J.Chen, T.Y.Roth, L.Morizono, H.Allewell, N.M.Tuchman, M.

(2007) Protein Sci 16: 1689-1699

  • DOI: https://doi.org/10.1110/ps.072919907
  • Primary Citation of Related Structures:  
    2G7M, 3L02, 3L04, 3L05, 3L06

  • PubMed Abstract: 

    Transcarbamylases catalyze the transfer of the carbamyl group from carbamyl phosphate (CP) to an amino group of a second substrate such as aspartate, ornithine, or putrescine. Previously, structural determination of a transcarbamylase from Xanthomonas campestris led to the discovery of a novel N-acetylornithine transcarbamylase (AOTCase) that catalyzes the carbamylation of N-acetylornithine. Recently, a novel N-succinylornithine transcarbamylase (SOTCase) from Bacteroides fragilis was identified. Structural comparisons of AOTCase from X. campestris and SOTCase from B. fragilis revealed that residue Glu92 (X. campestris numbering) plays a critical role in distinguishing AOTCase from SOTCase. Enzymatic assays of E92P, E92S, E92V, and E92A mutants of AOTCase demonstrate that each of these mutations converts the AOTCase to an SOTCase. Similarly, the P90E mutation in B. fragilis SOTCase (equivalent to E92 in X. campestris AOTCase) converts the SOTCase to AOTCase. Hence, a single amino acid substitution is sufficient to swap the substrate specificities of AOTCase and SOTCase. X-ray crystal structures of these mutants in complexes with CP and N-acetyl-L-norvaline (an analog of N-acetyl-L-ornithine) or N-succinyl-L-norvaline (an analog of N-succinyl-L-ornithine) substantiate this conversion. In addition to Glu92 (X. campestris numbering), other residues such as Asn185 and Lys30 in AOTCase, which are involved in binding substrates through bridging water molecules, help to define the substrate specificity of AOTCase. These results provide the correct annotation (AOTCase or SOTCase) for a set of the transcarbamylase-like proteins that have been erroneously annotated as ornithine transcarbamylase (OTCase, EC

  • Organizational Affiliation

    Children's National Medical Center, The George Washington University, Washington, DC 20010, USA. dshi@cnmcresearch.org

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
putative ornithine carbamoyltransferase338Bacteroides fragilisMutation(s): 2 
Gene Names: argF'
EC: 2.1.3
Find proteins for Q64Z33 (Bacteroides fragilis (strain YCH46))
Explore Q64Z33 
Go to UniProtKB:  Q64Z33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64Z33
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AN0

Download Ideal Coordinates CCD File 
G [auth X]
J [auth Y]
L [auth Z]
N [auth C]
Q [auth D]
G [auth X],
J [auth Y],
L [auth Z],
N [auth C],
Q [auth D],
S [auth E]
C7 H13 N O3
Query on CP

Download Ideal Coordinates CCD File 
H [auth X]
K [auth Y]
M [auth Z]
O [auth C]
R [auth D]
H [auth X],
K [auth Y],
M [auth Z],
O [auth C],
R [auth D],
T [auth E]
C H4 N O5 P
Query on SO4

Download Ideal Coordinates CCD File 
I [auth Y],
P [auth D]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.654α = 90
b = 156.654β = 90
c = 120.201γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description