4JZ8

Carbamate kinase from Giardia lamblia bound to citric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal Structures of Carbamate Kinase from Giardia lamblia Bound with Citric Acid and AMP-PNP.

Lim, K.Kulakova, L.Galkin, A.Herzberg, O.

(2013) PLoS One 8: e64004-e64004

  • DOI: 10.1371/journal.pone.0064004
  • Primary Citation of Related Structures:  
    4JZ7, 4JZ8, 4JZ9

  • PubMed Abstract: 
  • The parasite Giardia lamblia utilizes the L-arginine dihydrolase pathway to generate ATP from L-arginine. Carbamate kinase (CK) catalyzes the last step in this pathway, converting ADP and carbamoyl phosphate to ATP and ammonium carbamate. Because the L-arginine pathway is essential for G ...

    The parasite Giardia lamblia utilizes the L-arginine dihydrolase pathway to generate ATP from L-arginine. Carbamate kinase (CK) catalyzes the last step in this pathway, converting ADP and carbamoyl phosphate to ATP and ammonium carbamate. Because the L-arginine pathway is essential for G. lamblia survival and absent in high eukaryotes including humans, the enzyme is a potential target for drug development. We have determined two crystal structures of G. lamblia CK (glCK) with bound ligands. One structure, in complex with a nonhydrolyzable ATP analog, adenosine 5'-adenylyl-β,γ-imidodiphosphate (AMP-PNP), was determined at 2.6 Å resolution. The second structure, in complex with citric acid bound in the postulated carbamoyl phosphate binding site, was determined in two slightly different states at 2.1 and 2.4 Å resolution. These structures reveal conformational flexibility of an auxiliary domain (amino acid residues 123-170), which exhibits open or closed conformations or structural disorder, depending on the bound ligand. The structures also reveal a smaller conformational change in a region associated the AMP-PNP adenine binding site. The protein residues involved in binding, together with a model of the transition state, suggest that catalysis follows an in-line, predominantly dissociative, phosphotransfer reaction mechanism, and that closure of the flexible auxiliary domain is required to protect the transition state from bulk solvent.


    Related Citations: 
    • X-ray structure and characterization of carbamate kinase from the human parasite Giardia lamblia.
      Galkin, A., Kulakova, L., Wu, R., Nash, T.E., Dunaway-Mariano, D., Herzberg, O.
      (2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 386

    Organizational Affiliation

    Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbamate kinaseA, B, C, D317Giardia lamblia ATCC 50803Mutation(s): 0 
Gene Names: GL50803_16453GL50803_0016453
EC: 2.7.2.2
Find proteins for A8BB85 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
Explore A8BB85 
Go to UniProtKB:  A8BB85
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.928α = 90
b = 86.401β = 106.53
c = 101.96γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-04-02 
  • Released Date: 2013-06-05 
  • Deposition Author(s): Lim, K., Herzberg, O.

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release