1X9G

PUTATIVE MAR1 RIBONUCLEASE FROM LEISHMANIA DONOVANI

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Crystal structures and proposed structural/functional classification of three protozoan proteins from the isochorismatase superfamily.

Caruthers, J., Zucker, F., Worthey, E., Myler, P.J., Buckner, F., Van Voorhuis, W., Mehlin, C., Boni, E., Feist, T., Luft, J., Gulde, S., Lauricella, A., Kaluzhniy, O., Anderson, L., Le Trong, I., Holmes, M.A., Earnest, T., Soltis, M., Hodgson, K.O., Hol, W.G., Merritt, E.A.

(2005) Protein Sci. 14: 2887-2894

  • DOI: 10.1110/ps.051783005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • We have determined the crystal structures of three homologous proteins from the pathogenic protozoans Leishmania donovani, Leishmania major, and Trypanosoma cruzi. We propose that these proteins represent a new subfamily within the isochorismatase su ...

    We have determined the crystal structures of three homologous proteins from the pathogenic protozoans Leishmania donovani, Leishmania major, and Trypanosoma cruzi. We propose that these proteins represent a new subfamily within the isochorismatase superfamily (CDD classification cd004310). Their overall fold and key active site residues are structurally homologous both to the biochemically well-characterized N-carbamoylsarcosine-amidohydrolase, a cysteine hydrolase, and to the phenazine biosynthesis protein PHZD (isochorismase), an aspartyl hydrolase. All three proteins are annotated as mitochondrial-associated ribonuclease Mar1, based on a previous characterization of the homologous protein from L. tarentolae. This would constitute a new enzymatic activity for this structural superfamily, but this is not strongly supported by the observed structures. In these protozoan proteins, the extended active site is formed by inter-subunit association within a tetramer, which implies a distinct evolutionary history and substrate specificity from the previously characterized members of the isochorismatase superfamily. The characterization of the active site is supported crystallographically by the presence of an unidentified ligand bound at the active site cysteine of the T. cruzi structure.

    Organizational Affiliation: 

    Biomolecular Structure Center M/S 357742, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE MAR1
A
200Leishmania donovaniMutation(s): 0 
Find proteins for D0VWV0 (Leishmania donovani)
Go to UniProtKB:  D0VWV0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.225 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 147.438α = 90.00
b = 147.438β = 90.00
c = 147.438γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DMphasing
CNSrefinement
SOLVEphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2012-10-24
    Type: Database references
  • Version 1.4: 2019-07-24
    Type: Data collection, Refinement description