1BXR

STRUCTURE OF CARBAMOYL PHOSPHATE SYNTHETASE COMPLEXED WITH THE ATP ANALOG AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding.

Thoden, J.B.Wesenberg, G.Raushel, F.M.Holden, H.M.

(1999) Biochemistry 38: 2347-2357

  • DOI: https://doi.org/10.1021/bi982517h
  • Primary Citation of Related Structures:  
    1BXR

  • PubMed Abstract: 

    Carbamoyl phosphate synthetase (CPS) catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The catalytic mechanism of the enzyme occurs through three highly reactive intermediates: carboxyphosphate, ammonia, and carbamate. As isolated from Escherichia coli, CPS is an alpha, beta-heterodimeric protein with its three active sites separated by nearly 100 A. In addition, there are separate binding sites for the allosteric regulators, ornithine, and UMP. Given the sizable distances between the three active sites and the allosteric-binding pockets, it has been postulated that domain movements play key roles for intramolecular communication. Here we describe the structure of CPS from E. coli where, indeed, such a domain movement has occurred in response to nucleotide binding. Specifically, the protein was crystallized in the presence of a nonhydrolyzable analogue, AMPPNP, and its structure determined to 2.1 A resolution by X-ray crystallographic analysis. The B-domain of the carbamoyl phosphate synthetic component of the large subunit closes down over the active-site pocket such that some atoms move by more than 7 A relative to that observed in the original structure. The trigger for this movement resides in the hydrogen-bonding interactions between two backbone amide groups (Gly 721 and Gly 722) and the beta- and gamma-phosphate groups of the nucleotide triphosphate. Gly 721 and Gly 722 are located in a Type III' reverse turn, and this type of secondary structural motif is also observed in D-alanine:D-alanine ligase and glutathione synthetase, both of which belong to the "ATP-grasp" superfamily of proteins. Details concerning the geometries of the two active sites contained within the large subunit of CPS are described.


  • Organizational Affiliation

    Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53705, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CARBAMOYL-PHOSPHATE SYNTHASE
A, C, E, G
1,073Escherichia coliMutation(s): 0 
EC: 6.3.5.5
UniProt
Find proteins for P00968 (Escherichia coli (strain K12))
Explore P00968 
Go to UniProtKB:  P00968
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00968
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CARBAMOYL-PHOSPHATE SYNTHASE
B, D, F, H
382Escherichia coliMutation(s): 0 
EC: 6.3.5.5
UniProt
Find proteins for P0A6F1 (Escherichia coli (strain K12))
Explore P0A6F1 
Go to UniProtKB:  P0A6F1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6F1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
IA [auth C]
JA [auth C]
NB [auth G]
OB [auth G]
R [auth A]
IA [auth C],
JA [auth C],
NB [auth G],
OB [auth G],
R [auth A],
S [auth A],
YA [auth E],
ZA [auth E]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ORN
Query on ORN

Download Ideal Coordinates CCD File 
AB [auth E],
KA [auth C],
PB [auth G],
T [auth A]
L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
NET
Query on NET

Download Ideal Coordinates CCD File 
BB [auth E],
LA [auth C],
QB [auth G],
U [auth A]
TETRAETHYLAMMONIUM ION
C8 H20 N
CBXCPBUEXACCNR-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CB [auth G]
FB [auth G]
GB [auth G]
AA [auth C],
BA [auth C],
CB [auth G],
FB [auth G],
GB [auth G],
HA [auth C],
I [auth A],
L [auth A],
M [auth A],
OA [auth E],
RA [auth E],
SA [auth E],
X [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

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CA [auth C]
DB [auth G]
EB [auth G]
GA [auth C]
HB [auth G]
CA [auth C],
DB [auth G],
EB [auth G],
GA [auth C],
HB [auth G],
J [auth A],
K [auth A],
MB [auth G],
N [auth A],
NA [auth D],
PA [auth E],
QA [auth E],
RB [auth H],
TA [auth E],
W [auth B],
WA [auth E],
XA [auth E],
Y [auth C],
Z [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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DA [auth C]
EA [auth C]
FA [auth C]
IB [auth G]
JB [auth G]
DA [auth C],
EA [auth C],
FA [auth C],
IB [auth G],
JB [auth G],
KB [auth G],
LB [auth G],
MA [auth D],
O [auth A],
P [auth A],
Q [auth A],
UA [auth E],
V [auth B],
VA [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
ANP PDBBind:  1BXR Ki: 4.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.9α = 90
b = 164.5β = 90
c = 332.6γ = 90
Software Package:
Software NamePurpose
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Other, Refinement description