3L05

Crystal structure of N-acetyl-L-ornithine transcarbamylase E92S mutant complexed with carbamyl phosphate and N-succinyl-L-norvaline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  
    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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acetylornithine carbamoyltransferaseA359Xanthomonas campestris pv. campestris str. ATCC 33913Mutation(s): 1 
Gene Names: argFargF'XCC2249
EC: 2.1.3.9
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SN0
Query on SN0

Download CCD File 
A
N-(3-CARBOXYPROPANOYL)-L-NORVALINE
C9 H15 N O5
HRAPDLBXHOBAKA-LURJTMIESA-N
 Ligand Interaction
CP
Query on CP

Download CCD File 
A
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
C H4 N O5 P
FFQKYPRQEYGKAF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
AL-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.184 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.974α = 90
b = 128.974β = 90
c = 128.974γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description