1CE8

CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIS COLI WITH COMPLEXED WITH THE ALLOSTERIC LIGAND IMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase.

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

(1999) J Biol Chem 274: 22502-22507

  • DOI: https://doi.org/10.1074/jbc.274.32.22502
  • Primary Citation of Related Structures:  
    1CE8

  • PubMed Abstract: 

    Carbamoyl phosphate synthetase (CPS) from Escherichia coli catalyzes the formation of carbamoyl phosphate, which is subsequently employed in both the pyrimidine and arginine biosynthetic pathways. The reaction mechanism is known to proceed through at least three highly reactive intermediates: ammonia, carboxyphosphate, and carbamate. In keeping with the fact that the product of CPS is utilized in two competing metabolic pathways, the enzyme is highly regulated by a variety of effector molecules including potassium and ornithine, which function as activators, and UMP, which acts as an inhibitor. IMP is also known to bind to CPS but the actual effect of this ligand on the activity of the enzyme is dependent upon both temperature and assay conditions. Here we describe the three-dimensional architecture of CPS with bound IMP determined and refined to 2.1 A resolution. The nucleotide is situated at the C-terminal portion of a five-stranded parallel beta-sheet in the allosteric domain formed by Ser(937) to Lys(1073). Those amino acid side chains responsible for anchoring the nucleotide to the polypeptide chain include Lys(954), Thr(974), Thr(977), Lys(993), Asn(1015), and Thr(1017). A series of hydrogen bonds connect the IMP-binding pocket to the active site of the large subunit known to function in the phosphorylation of the unstable intermediate, carbamate. This structural analysis reveals, for the first time, the detailed manner in which CPS accommodates nucleotide monophosphate effector molecules within the allosteric domain.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (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
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
DC [auth G]
EC [auth G]
JB [auth E]
KB [auth E]
PA [auth C]
DC [auth G],
EC [auth G],
JB [auth E],
KB [auth E],
PA [auth C],
QA [auth C],
V [auth A],
W [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
IMP
Query on IMP

Download Ideal Coordinates CCD File 
GC [auth G],
MB [auth E],
SA [auth C],
Y [auth A]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
ORN
Query on ORN

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AA [auth A]
FC [auth G]
IC [auth G]
LB [auth E]
OB [auth E]
AA [auth A],
FC [auth G],
IC [auth G],
LB [auth E],
OB [auth E],
RA [auth C],
UA [auth C],
X [auth A]
L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
NET
Query on NET

Download Ideal Coordinates CCD File 
HC [auth G],
NB [auth E],
TA [auth C],
Z [auth A]
TETRAETHYLAMMONIUM ION
C8 H20 N
CBXCPBUEXACCNR-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
CC [auth G],
IB [auth E],
OA [auth C],
U [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN
Query on MN

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BB [auth E]
CA [auth C]
DA [auth C]
HA [auth C]
I [auth A]
BB [auth E],
CA [auth C],
DA [auth C],
HA [auth C],
I [auth A],
J [auth A],
N [auth A],
QB [auth G],
RB [auth G],
VB [auth G],
WA [auth E],
XA [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AB [auth E]
BA [auth B]
CB [auth E]
DB [auth E]
EA [auth C]
AB [auth E],
BA [auth B],
CB [auth E],
DB [auth E],
EA [auth C],
EB [auth E],
FA [auth C],
GA [auth C],
IA [auth C],
JA [auth C],
JC [auth H],
K [auth A],
KA [auth C],
L [auth A],
M [auth A],
O [auth A],
P [auth A],
PB [auth F],
Q [auth A],
SB [auth G],
TB [auth G],
UB [auth G],
VA [auth D],
WB [auth G],
XB [auth G],
YA [auth E],
YB [auth G],
ZA [auth E]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AC [auth G]
BC [auth G]
FB [auth E]
GB [auth E]
HB [auth E]
AC [auth G],
BC [auth G],
FB [auth E],
GB [auth E],
HB [auth E],
LA [auth C],
MA [auth C],
NA [auth C],
R [auth A],
S [auth A],
T [auth A],
ZB [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.1α = 90
b = 163.9β = 90
c = 331.2γ = 90
Software Package:
Software NamePurpose
AMoREphasing
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: 1999-07-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Derived calculations
  • Version 1.4: 2022-12-21
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-09-20
    Changes: Data collection, Refinement description