1C30

CRYSTAL STRUCTURE OF CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT MUTATION C269S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The small subunit of carbamoyl phosphate synthetase: snapshots along the reaction pathway.

Thoden, J.B.Huang, X.Raushel, F.M.Holden, H.M.

(1999) Biochemistry 38: 16158-16166

  • DOI: https://doi.org/10.1021/bi991741j
  • Primary Citation of Related Structures:  
    1C30, 1C3O, 1CS0

  • PubMed Abstract: 

    Carbamoyl phosphate synthetase (CPS) plays a key role in both arginine and pyrimidine biosynthesis by catalyzing the production of carbamoyl phosphate. The enzyme from Escherichi coli consists of two polypeptide chains referred to as the small and large subunits. On the basis of both amino acid sequence analyses and X-ray structural studies, it is known that the small subunit belongs to the Triad or Type I class of amidotransferases, all of which contain a cysteine-histidine (Cys269 and His353) couple required for activity. The hydrolysis of glutamine by the small subunit has been proposed to occur via two tetrahedral intermediates and a glutamyl-thioester moiety. Here, we describe the three-dimensional structures of the C269S/glutamine and CPS/glutamate gamma-semialdehyde complexes, which serve as mimics for the Michaelis complex and the tetrahedral intermediates, respectively. In conjunction with the previously solved glutamyl-thioester intermediate complex, the stereochemical course of glutamine hydrolysis in CPS has been outlined. Specifically, attack by the thiolate of Cys269 occurs at the Si face of the carboxamide group of the glutamine substrate leading to a tetrahedral intermediate with an S-configuration. Both the backbone amide groups of Gly241 and Leu270, and O(gamma) of Ser47 play key roles in stabilizing the developing oxyanion. Collapse of the tetrahedral intermediate leads to formation of the glutamyl-thioester intermediate, which is subsequently attacked at the Si face by an activated water molecule positioned near His353. The results described here serve as a paradigm for other members of the Triad class of amidotranferases.


  • Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison 53705, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT
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 SYNTHETASE: SMALL SUBUNIT
B, D, F, H
382Escherichia coliMutation(s): 1 
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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
HC [auth G]
IC [auth G]
OB [auth E]
AA [auth A],
BA [auth A],
HC [auth G],
IC [auth G],
OB [auth E],
PB [auth E],
UA [auth C],
VA [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ORN
Query on ORN

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W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
NET
Query on NET

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CA [auth A],
JC [auth G],
QB [auth E],
WA [auth C]
TETRAETHYLAMMONIUM ION
C8 H20 N
CBXCPBUEXACCNR-UHFFFAOYSA-N
PO4
Query on PO4

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GC [auth G]
MB [auth E]
NB [auth E]
SA [auth C]
TA [auth C]
GC [auth G],
MB [auth E],
NB [auth E],
SA [auth C],
TA [auth C],
V [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN
Query on MN

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BB [auth E]
CB [auth E]
FA [auth C]
FB [auth E]
GA [auth C]
BB [auth E],
CB [auth E],
FA [auth C],
FB [auth E],
GA [auth C],
I [auth A],
J [auth A],
JA [auth C],
M [auth A],
TB [auth G],
UB [auth G],
XB [auth G]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AB [auth E]
DB [auth E]
DC [auth G]
EA [auth B]
EB [auth E]
AB [auth E],
DB [auth E],
DC [auth G],
EA [auth B],
EB [auth E],
EC [auth G],
FC [auth G],
GB [auth E],
HA [auth C],
HB [auth E],
IA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
LB [auth E],
LC [auth H],
N [auth A],
O [auth A],
PA [auth C],
QA [auth C],
RA [auth C],
S [auth A],
SB [auth F],
T [auth A],
U [auth A],
VB [auth G],
WB [auth G],
YA [auth D],
YB [auth G],
ZA [auth E],
ZB [auth G]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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AC [auth G]
BC [auth G]
CC [auth G]
DA [auth B]
IB [auth E]
AC [auth G],
BC [auth G],
CC [auth G],
DA [auth B],
IB [auth E],
JB [auth E],
KB [auth E],
KC [auth H],
MA [auth C],
NA [auth C],
OA [auth C],
P [auth A],
Q [auth A],
R [auth A],
RB [auth F],
XA [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.6α = 90
b = 164.6β = 90
c = 332.7γ = 90
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement
d*TREKdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-10
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-03-14
    Changes: Database references
  • Version 1.4: 2019-11-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-07
    Changes: Data collection, Database references, Derived calculations