2G7M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1110/ps.072919907
  • Primary Citation of Related Structures:  

  • 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 Xanthomona ...

    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 2.1.3.3).


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
putative ornithine carbamoyltransferase
X, Y, Z, C, D, E
338Bacteroides fragilis (strain YCH46)Mutation(s): 2 
Find proteins for Q64Z33 (Bacteroides fragilis (strain YCH46))
Go to UniProtKB:  Q64Z33
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
D, Y
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CP
Query on CP

Download SDF File 
Download CCD File 
C, D, E, X, Y, Z
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
C H4 N O5 P
FFQKYPRQEYGKAF-UHFFFAOYSA-N
 Ligand Interaction
AN0
Query on AN0

Download SDF File 
Download CCD File 
C, D, E, X, Y, Z
N-ACETYL-L-NORVALINE
C7 H13 N O3
BSYFPUSAWVWWDG-LURJTMIESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.218 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 156.654α = 90.00
b = 156.654β = 90.00
c = 120.201γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description