1A9X

CARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HYDROLYSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis.

Thoden, J.B.Miran, S.G.Phillips, J.C.Howard, A.J.Raushel, F.M.Holden, H.M.

(1998) Biochemistry 37: 8825-8831

  • DOI: 10.1021/bi9807761
  • Primary Citation of Related Structures:  
    1A9X

  • PubMed Abstract: 
  • Carbamoyl phosphate synthetase from Escherichia coli catalyzes the production of carbamoyl phosphate from two molecules of Mg2+ATP, one molecule of bicarbonate, and one molecule of glutamine. The enzyme consists of two polypeptide chains referred to as the large and small subunits ...

    Carbamoyl phosphate synthetase from Escherichia coli catalyzes the production of carbamoyl phosphate from two molecules of Mg2+ATP, one molecule of bicarbonate, and one molecule of glutamine. The enzyme consists of two polypeptide chains referred to as the large and small subunits. While the large subunit provides the active sites responsible for the binding of nucleotides and other effector ligands, the small subunit contains those amino acid residues that catalyze the hydrolysis of glutamine to glutamate and ammonia. From both amino acid sequence analyses and structural studies it is now known that the small subunit belongs to the class I amidotransferase family of enzymes. Numerous biochemical studies have suggested that the reaction mechanism of the small subunit proceeds through the formation of the glutamyl thioester intermediate and that both Cys 269 and His 353 are critical for catalysis. Here we describe the X-ray crystallographic structure of carbamoyl phosphate synthetase from E. coli in which His 353 has been replaced with an asparagine residue. Crystals employed in the investigation were grown in the presence of glutamine, and the model has been refined to a crystallographic R-factor of 19.1% for all measured X-ray data from 30 to 1.8 A resolution. The active site of the small subunit clearly contains a covalently bound thioester intermediate at Cys 269, and indeed, this investigation provides the first direct structural observation of an enzyme intermediate in the amidotransferase family.


    Organizational Affiliation

    Institute for Enzyme Research, The Graduate School, University of Wisconsin-Madison 53705, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)A, C, E, G1073Escherichia coliMutation(s): 0 
EC: 6.3.5.5
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 CHAIN)B, D, F, H379Escherichia coliMutation(s): 2 
EC: 6.3.5.5
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 
BC [auth E], BD [auth G], CA [auth A], CB [auth C], CC [auth E], CD [auth G], DA [auth A], DB [auth C]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ORN
Query on ORN

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DC [auth E], DD [auth G], EA [auth A], EB [auth C]L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
 Ligand Interaction
NET
Query on NET

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EC [auth E], ED [auth G], FA [auth A], FB [auth C]TETRAETHYLAMMONIUM ION
C8 H20 N
CBXCPBUEXACCNR-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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AB [auth C] , AC [auth E] , AD [auth G] , BB [auth C] , I [auth A] , J [auth A] , K [auth A] , LC [auth G] , 
AB [auth C],  AC [auth E],  AD [auth G],  BB [auth C],  I [auth A],  J [auth A],  K [auth A],  LC [auth G],  MA [auth C],  MB [auth E],  P [auth A],  YC [auth G],  ZA [auth C],  ZB [auth E],  ZC [auth G]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MN
Query on MN

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HC [auth G] , IA [auth C] , IB [auth E] , IC [auth G] , JA [auth C] , JB [auth E] , L [auth A] , M [auth A] , 
HC [auth G],  IA [auth C],  IB [auth E],  IC [auth G],  JA [auth C],  JB [auth E],  L [auth A],  M [auth A],  MC [auth G],  NA [auth C],  NB [auth E],  Q [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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AA [auth A] , BA [auth A] , GC [auth F] , GD [auth H] , HA [auth B] , HB [auth D] , JC [auth G] , KA [auth C] , 
AA [auth A],  BA [auth A],  GC [auth F],  GD [auth H],  HA [auth B],  HB [auth D],  JC [auth G],  KA [auth C],  KB [auth E],  KC [auth G],  LA [auth C],  LB [auth E],  N [auth A],  NC [auth G],  O [auth A],  OA [auth C],  OB [auth E],  OC [auth G],  PA [auth C],  PB [auth E],  R [auth A],  S [auth A],  VC [auth G],  WA [auth C],  WB [auth E],  WC [auth G],  XA [auth C],  XB [auth E],  XC [auth G],  YA [auth C],  YB [auth E],  Z [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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FC [auth F] , FD [auth H] , GA [auth B] , GB [auth D] , PC [auth G] , QA [auth C] , QB [auth E] , QC [auth G] , 
FC [auth F],  FD [auth H],  GA [auth B],  GB [auth D],  PC [auth G],  QA [auth C],  QB [auth E],  QC [auth G],  RA [auth C],  RB [auth E],  RC [auth G],  SA [auth C],  SB [auth E],  SC [auth G],  T [auth A],  TA [auth C],  TB [auth E],  TC [auth G],  U [auth A],  UA [auth C],  UB [auth E],  UC [auth G],  V [auth A],  VA [auth C],  VB [auth E],  W [auth A],  X [auth A],  Y [auth A]
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: 1.80 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.1α = 90
b = 164.4β = 90
c = 332.3γ = 90
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement
SAINTdata reduction
XCALIBREdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1998-04-14 
  • Released Date: 1998-10-21 
  • Deposition Author(s): Thoden, J., Holden, H.

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-03-10
    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