3KZO

Crystal structure of N-acetyl-L-ornithine transcarbamylase complexed with carbamyl phosphate and N-acetyl-L-norvaline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structures of N-acetylornithine transcarbamoylase from Xanthomonas campestris complexed with substrates and substrate analogs imply mechanisms for substrate binding and catalysis.

Shi, D.Yu, X.Roth, L.Morizono, H.Tuchman, M.Allewell, N.M.

(2006) Proteins 64: 532-542

  • DOI: https://doi.org/10.1002/prot.21013
  • Primary Citation of Related Structures:  
    3KZM, 3KZN, 3KZO

  • PubMed Abstract: 

    N-acetyl-L-ornithine transcarbamoylase (AOTCase) is a new member of the transcarbamoylase superfamily that is essential for arginine biosynthesis in several eubacteria. We report here crystal structures of the binary complexes of AOTCase with its substrates, carbamoyl phosphate (CP) or N-acetyl-L-ornithine (AORN), and the ternary complex with CP and N-acetyl-L-norvaline. Comparison of these structures demonstrates that the substrate-binding mechanism of this novel transcarbamoylase is different from those of aspartate and ornithine transcarbamoylases, both of which show ordered substrate binding with large domain movements. CP and AORN bind to AOTCase independently, and the main conformational change upon substrate binding is ordering of the 80's loop, with a small domain closure around the active site and little movement of the 240's loop. The structures of the complexes provide insight into the mode of substrate binding and the mechanism of the transcarbamoylation reaction.


  • Organizational Affiliation

    Children's National Medical Center, Washington, DC 20010-2970, USA. dshi@cnmcresearch.org


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetylornithine carbamoyltransferase359Xanthomonas campestris pv. campestris str. ATCC 33913Mutation(s): 0 
Gene Names: argFargF'XCC2249
EC: 2.1.3.9
UniProt
Find proteins for Q8P8J2 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25))
Explore Q8P8J2 
Go to UniProtKB:  Q8P8J2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8P8J2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.953α = 90
b = 129.953β = 90
c = 129.953γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-22
    Changes: Data collection