1CS0

Crystal structure of carbamoyl phosphate synthetase complexed at CYS269 in the small subunit with the tetrahedral mimic l-glutamate gamma-semialdehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 10.1021/bi991741j
  • Primary Citation of Related Structures:  
    1CS0, 1C30, 1C3O

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNITA, 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
CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNITB, 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
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth A], SC [auth G], TC [auth G], VB [auth E], WA [auth C], WB [auth E], XA [auth C], Z [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ORN
Query on ORN

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BA [auth A], UC [auth G], XB [auth E], YA [auth C]L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
 Ligand Interaction
NET
Query on NET

Download Ideal Coordinates CCD File 
CA [auth A], VC [auth G], YB [auth E], ZA [auth C]TETRAETHYLAMMONIUM ION
C8 H20 N
CBXCPBUEXACCNR-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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RC [auth G], TB [auth E], UB [auth E], VA [auth C], Y [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MN
Query on MN

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FC [auth G] , GA [auth C] , GC [auth G] , HA [auth C] , I [auth A] , J [auth A] , JC [auth G] , KA [auth C] , 
FC [auth G],  GA [auth C],  GC [auth G],  HA [auth C],  I [auth A],  J [auth A],  JC [auth G],  KA [auth C],  M [auth A],  MB [auth E],  NB [auth E],  QB [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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BC [auth F] , CB [auth D] , CC [auth G] , DC [auth G] , EC [auth G] , FA [auth B] , HC [auth G] , IA [auth C] , 
BC [auth F],  CB [auth D],  CC [auth G],  DC [auth G],  EC [auth G],  FA [auth B],  HC [auth G],  IA [auth C],  IB [auth E],  IC [auth G],  JA [auth C],  JB [auth E],  K [auth A],  KB [auth E],  KC [auth G],  L [auth A],  LA [auth C],  LB [auth E],  LC [auth G],  MA [auth C],  N [auth A],  O [auth A],  OB [auth E],  PB [auth E],  RB [auth E],  SA [auth C],  SB [auth E],  TA [auth C],  UA [auth C],  V [auth A],  W [auth A],  WC [auth H],  X [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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AB [auth D] , AC [auth F] , BB [auth D] , DA [auth B] , DB [auth E] , EA [auth B] , EB [auth E] , FB [auth E] , 
AB [auth D],  AC [auth F],  BB [auth D],  DA [auth B],  DB [auth E],  EA [auth B],  EB [auth E],  FB [auth E],  GB [auth E],  HB [auth E],  MC [auth G],  NA [auth C],  NC [auth G],  OA [auth C],  OC [auth G],  P [auth A],  PA [auth C],  PC [auth G],  Q [auth A],  QA [auth C],  QC [auth G],  R [auth A],  RA [auth C],  S [auth A],  T [auth A],  U [auth A],  XC [auth H],  YC [auth H],  ZB [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CYG
Query on CYG
B, D, F, HL-PEPTIDE LINKINGC8 H14 N2 O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.7α = 90
b = 163.8β = 90
c = 332.6γ = 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: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Derived calculations