1JDB

CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIA COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution.

Thoden, J.B.Raushel, F.M.Benning, M.M.Rayment, I.Holden, H.M.

(1999) Acta Crystallogr.,Sect.D 55: 8-24

  • DOI: 10.1107/S0907444998006234

  • PubMed Abstract: 
  • Carbamoyl phosphate synthetase catalyzes the formation of carbamoyl phosphate from one molecule of bicarbonate, two molecules of Mg2+ATP and one molecule of glutamine or ammonia depending upon the particular form of the enzyme under investigation. As ...

    Carbamoyl phosphate synthetase catalyzes the formation of carbamoyl phosphate from one molecule of bicarbonate, two molecules of Mg2+ATP and one molecule of glutamine or ammonia depending upon the particular form of the enzyme under investigation. As isolated from Escherichia coli, the enzyme is an alpha,beta-heterodimer consisting of a small subunit that hydrolyzes glutamine and a large subunit that catalyzes the two required phosphorylation events. Here the three-dimensional structure of carbamoyl phosphate synthetase from E. coli refined to 2.1 A resolution with an R factor of 17.9% is described. The small subunit is distinctly bilobal with a catalytic triad (Cys269, His353 and Glu355) situated between the two structural domains. As observed in those enzymes belonging to the alpha/beta-hydrolase family, the active-site nucleophile, Cys269, is perched at the top of a tight turn. The large subunit consists of four structural units: the carboxyphosphate synthetic component, the oligomerization domain, the carbamoyl phosphate synthetic component and the allosteric domain. Both the carboxyphosphate and carbamoyl phosphate synthetic components bind Mn2+ADP. In the carboxyphosphate synthetic component, the two observed Mn2+ ions are both octahedrally coordinated by oxygen-containing ligands and are bridged by the carboxylate side chain of Glu299. Glu215 plays a key allosteric role by coordinating to the physiologically important potassium ion and hydrogen bonding to the ribose hydroxyl groups of ADP. In the carbamoyl phosphate synthetic component, the single observed Mn2+ ion is also octahedrally coordinated by oxygen-containing ligands and Glu761 plays a similar role to that of Glu215. The carboxyphosphate and carbamoyl phosphate synthetic components, while topologically equivalent, are structurally different, as would be expected in light of their separate biochemical functions.


    Related Citations: 
    • Structure of Carbamoyl Phosphate Synthetase: A Journey of 96 a from Substrate to Product
      Thoden, J.B.,Holden, H.M.,Wesenberg, G.,Raushel, F.M.,Rayment, I.
      (1997) Biochemistry 36: 6305


    Organizational Affiliation

    Institute for Enzyme Research, The Graduate School, and Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 1710 University Avenue, Madison, Wisconsin 53705, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBAMOYL PHOSPHATE SYNTHETASE
B, E, H, K
1073Escherichia coli (strain K12)Gene Names: carB (pyrA)
EC: 6.3.5.5
Find proteins for P00968 (Escherichia coli (strain K12))
Go to UniProtKB:  P00968
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CARBAMOYL PHOSPHATE SYNTHETASE
C, F, I, L
382Escherichia coli (strain K12)Gene Names: carA (pyrA)
EC: 6.3.5.5
Find proteins for P0A6F1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6F1
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B, C, E, F, H, I, K, L
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
B, E, H, K
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
B, E, H, K
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
B, E, H, K
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B, C, E, F, H, I, K, L
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GLN
Query on GLN

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Download CCD File 
B, E, H, K
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
NET
Query on NET

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Download CCD File 
B, E, H, K
TETRAETHYLAMMONIUM ION
C8 H20 N
CBXCPBUEXACCNR-UHFFFAOYSA-N
 Ligand Interaction
ORN
Query on ORN

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Download CCD File 
B, E, H, K
L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 143.800α = 90.00
b = 167.700β = 90.00
c = 323.000γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance