2WE5

Carbamate kinase from Enterococcus faecalis bound to MgADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Substrate Binding and Catalysis in Carbamate Kinase Ascertained by Crystallographic and Site- Directed Mutagenesis Studies. Movements and Significance of a Unique Globular Subdomain of This Key Enzyme for Fermentative ATP Production in Bacteria.

Ramon-Maiques, S.Marina, A.Guinot, A.Gil-Ortiz, F.Uriarte, M.Fita, I.Rubio, V.

(2010) J.Mol.Biol. 397: 1261

  • DOI: 10.1016/j.jmb.2010.02.038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Carbamate kinase (CK) makes ATP from ADP and carbamoyl phosphate (CP) in the final step of the microbial fermentative catabolism of arginine, agmatine, and oxalurate/allantoin. Two previously reported CK structures failed to clarify CP binding and ca ...

    Carbamate kinase (CK) makes ATP from ADP and carbamoyl phosphate (CP) in the final step of the microbial fermentative catabolism of arginine, agmatine, and oxalurate/allantoin. Two previously reported CK structures failed to clarify CP binding and catalysis and to reveal the significance of the protruding subdomain (PSD) that hangs over the CK active center as an exclusive and characteristic CK feature. We clarify now these three questions by determining two crystal structures of Enterococcus faecalis CK (one at 1.5 A resolution and containing bound MgADP, and the other at 2.1 A resolution and having in the active center one sulfate and two fixed water molecules that mimic one bound CP molecule) and by mutating active-center residues, determining the consequences of these mutations on enzyme functionality. Superimposition of the present crystal structures reconstructs the filled active center in the ternary complex, immediately suggesting in-line associative phosphoryl group transfer and a mechanism for enzyme catalysis involving N51, K209, K271, D210, and the PSD residue K128. The large respective increases and decreases in K(m)(CP) and k(cat) triggered by the mutations N51A, K128A, K209A, and D210N corroborate the ternary complex active-site architecture and the catalytic mechanism proposed. The extreme negative effects of K128A demonstrate a key role of the PSD in substrate binding and catalysis. The crystal structures reveal large rigid-body movements of the PSD towards the enzyme body that place K128 next to CP and bury the CP site. A mechanism that connects CP site occupation with the PSD approach, involving V206-I207 in the CP site and P162-S163 in the PSD stem, is identified. The effects of the V206A and V206L mutations support this mechanism. It is concluded that the PSD movement allows CK to select against the abundant CP/carbamate analogues acetylphosphate/acetate and bicarbonate, rendering CK highly selective for CP/carbamate.


    Related Citations: 
    • Carbamate Kinase: New Structural Machinery for Making Carbamoyl Phosphate, the Common Precursor of Pyrimidines and Arginine.
      Marina, A.,Alzari, P.M.,Bravo, J.,Uriarte, M.,Barcelona, B.,Fita, I.,Rubio, V.
      (1999) Protein Sci. 8: 934
    • The 1.5 A Resolution Crystal Structure of the Carbamate Kinase-Like Carbamoyl Phosphate Synthetase from the Hyperthermophilic Archaeon Pyrococcus Furiosus, Bound to Adp, Confirms that This Thermostable Enzyme is a Carbamate Kinase, and Provides Insight Into Substrate Binding and Stability in Carbamate Kinases.
      Ramon-Maiques, S.,Marina, A.,Uriarte, M.,Fita, I.,Rubio, V.
      (2000) J.Mol.Biol. 299: 463


    Organizational Affiliation

    Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (Instituto de Salud Carlos III), Jaime Roig 11, Valencia 46010, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBAMATE KINASE 1
A, B, C
310Enterococcus faecalis (strain ATCC 700802 / V583)Mutation(s): 0 
Gene Names: arcC1 (arcC, arcC-1)
EC: 2.7.2.2
Find proteins for P0A2X7 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  P0A2X7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.201 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.522α = 90.00
b = 103.522β = 90.00
c = 155.414γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
AMoREphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references, Derived calculations, Other, Structure summary, Version format compliance
  • Version 1.2: 2019-04-03
    Type: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation
  • Version 1.4: 2019-07-24
    Type: Data collection