Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 22.70 kDa 
• Atom Count: 1517 
• Modelled Residue Count: 192 
• Deposited Residue Count: 200 
• Unique protein chains: 1

1X9G

PUTATIVE MAR1 RIBONUCLEASE FROM LEISHMANIA DONOVANI

• PDB DOI: 10.2210/pdb1X9G/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Leishmania donovani
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-20 Released: 2004-09-07 
• Deposition Author(s): Caruthers, J., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.276 
• R-Value Work: 0.225 
• R-Value Observed: 0.230 

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

• PubMed: 16199669 
• DOI: 10.1110/ps.051783005
• Primary Citation of Related Structures:  
  1X9G, 1XN4, 1YZV


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE MAR1	A	200	Leishmania donovani	Mutation(s): 0  Gene Names: CGC20_23995, CGC21_10020, LdCL_120005600, LDHU3_12.0090
UniProt
Find proteins for D0VWV0 (Leishmania donovani) Explore D0VWV0  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 
• R-Value Observed: 0.230 
• Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.438	α = 90
b = 147.438	β = 90
c = 147.438	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
SOLVE	phasing
DM	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-20 
• Released Date: 2004-09-07 
Deposition Author(s): Caruthers, J., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

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