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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)A, C, E, G1073Escherichia coliMutation(s): 0 
EC: 6.3.5.5
UniProt
Find proteins for P00968 (Escherichia coli (strain K12))
Explore P00968 
Go to UniProtKB:  P00968
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)B, D, F, H382Escherichia coliMutation(s): 0 
EC: 6.3.5.5
UniProt
Find proteins for P0A6F1 (Escherichia coli (strain K12))
Explore P0A6F1 
Go to UniProtKB:  P0A6F1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / 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], QA [auth C], V [auth A], W [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
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
 Ligand Interaction
ORN
Query on ORN

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
MN
Query on MN

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BB [auth E] , CA [auth C] , DA [auth C] , HA [auth C] , I [auth A] , J [auth A] , N [auth A] , QB [auth G] , 
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
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
AB [auth E] , BA [auth B] , CB [auth E] , DB [auth E] , EA [auth C] , EB [auth E] , FA [auth C] , GA [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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AC [auth G] , BC [auth G] , FB [auth E] , GB [auth E] , HB [auth E] , LA [auth C] , MA [auth C] , NA [auth C] , 
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
 Ligand Interaction
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