1M6V

Crystal Structure of the G359F (small subunit) Point Mutant of Carbamoyl Phosphate Synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Carbamoyl-phosphate synthetase. Creation of an escape route for ammonia

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

(2002) J Biol Chem 277: 39722-39727

  • DOI: 10.1074/jbc.M206915200
  • Primary Citation of Related Structures:  
    1M6V

  • PubMed Abstract: 
  • Carbamoyl-phosphate synthetase catalyzes the production of carbamoyl phosphate through a reaction mechanism requiring one molecule of bicarbonate, two molecules of MgATP, and one molecule of glutamine. The enzyme from Escherichia coli is composed of two polypeptide chains ...

    Carbamoyl-phosphate synthetase catalyzes the production of carbamoyl phosphate through a reaction mechanism requiring one molecule of bicarbonate, two molecules of MgATP, and one molecule of glutamine. The enzyme from Escherichia coli is composed of two polypeptide chains. The smaller of these belongs to the Class I amidotransferase superfamily and contains all of the necessary amino acid side chains required for the hydrolysis of glutamine to glutamate and ammonia. Two homologous domains from the larger subunit adopt conformations that are characteristic for members of the ATP-grasp superfamily. Each of these ATP-grasp domains contains an active site responsible for binding one molecule of MgATP. High resolution x-ray crystallographic analyses have shown that, remarkably, the three active sites in the E. coli enzyme are connected by a molecular tunnel of approximately 100 A in total length. Here we describe the high resolution x-ray crystallographic structure of the G359F (small subunit) mutant protein of carbamoyl phosphate synthetase. This residue was initially targeted for study because it resides within the interior wall of the molecular tunnel leading from the active site of the small subunit to the first active site of the large subunit. It was anticipated that a mutation to the larger residue would "clog" the ammonia tunnel and impede the delivery of ammonia from its site of production to the site of utilization. In fact, the G359F substitution resulted in a complete change in the conformation of the loop delineated by Glu-355 to Ala-364, thereby providing an "escape" route for the ammonia intermediate directly to the bulk solvent. The substitution also effected the disposition of several key catalytic amino acid side chains in the small subunit active site.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706-1544, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
carbamoyl phosphate synthetase large chainA, C, E, G1073Escherichia coliMutation(s): 0 
Gene Names: carB
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
carbamoyl-phosphate synthetase small chainB, D, F, H382Escherichia coliMutation(s): 1 
Gene Names: carA
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
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 
LC [auth G],
MC [auth G],
PB [auth E],
QB [auth E],
TA [auth C],
LC [auth G],
MC [auth G],
PB [auth E],
QB [auth E],
TA [auth C],
UA [auth C],
W [auth A],
X [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ORN
Query on ORN

Download Ideal Coordinates CCD File 
NC [auth G],
RB [auth E],
VA [auth C],
Y [auth A]
L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
 Ligand Interaction
NET
Query on NET

Download Ideal Coordinates CCD File 
OC [auth G],
SB [auth E],
WA [auth C],
Z [auth A]
TETRAETHYLAMMONIUM ION
C8 H20 N
CBXCPBUEXACCNR-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
KC [auth G],
OB [auth E],
SA [auth C],
V [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
AB [auth E],
CA [auth C],
DA [auth C],
DB [auth E],
GA [auth C],
AB [auth E],
CA [auth C],
DA [auth C],
DB [auth E],
GA [auth C],
I [auth A],
J [auth A],
M [auth A],
VB [auth G],
WB [auth G],
ZA [auth E],
ZB [auth G]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth B],
AC [auth G],
BB [auth E],
BC [auth G],
CB [auth E],
AA [auth B],
AC [auth G],
BB [auth E],
BC [auth G],
CB [auth E],
CC [auth G],
DC [auth G],
EA [auth C],
EB [auth E],
FA [auth C],
FB [auth E],
GB [auth E],
HA [auth C],
HB [auth E],
IA [auth C],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
N [auth A],
O [auth A],
P [auth A],
TB [auth F],
XA [auth D],
XB [auth G],
YB [auth G]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth B],
EC [auth G],
FC [auth G],
GC [auth G],
HC [auth G],
BA [auth B],
EC [auth G],
FC [auth G],
GC [auth G],
HC [auth G],
IB [auth E],
IC [auth G],
JB [auth E],
JC [auth G],
KB [auth E],
LA [auth C],
LB [auth E],
MA [auth C],
MB [auth E],
NA [auth C],
NB [auth E],
OA [auth C],
PA [auth C],
PC [auth H],
Q [auth A],
QA [auth C],
R [auth A],
RA [auth C],
S [auth A],
T [auth A],
U [auth A],
UB [auth F],
YA [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.5α = 90
b = 164.2β = 90
c = 331.5γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
HKL-2000data reduction
TNTrefinement
d*TREKdata reduction
HKL-2000data scaling
TNTphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-31
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Derived calculations
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations