6V99

Agrobacterium tumefaciens ADP-Glucose pyrophosphorylase- S72D in the presence of sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Site-directed mutagenesis of Serine-72 reveals the location of the fructose 6-phosphate regulatory site of the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase.

Alghamdi, M.A.Hussien, R.A.Zheng, Y.Patel, H.P.Asencion Diez, M.D.A Iglesias, A.Liu, D.Ballicora, M.A.

(2022) Protein Sci 31: e4376-e4376

  • DOI: 10.1002/pro.4376
  • Primary Citation of Related Structures:  
    6V96, 6V99, 6V9A

  • PubMed Abstract: 
  • The allosteric regulation of ADP-glucose pyrophosphorylase is critical for the biosynthesis of glycogen in bacteria and starch in plants. The enzyme from Agrobacterium tumefaciens is activated by fructose 6-phosphate (Fru6P) and pyruvate (Pyr). The Pyr site has been recently found, but the site where Fru6P binds has remained unknown ...

    The allosteric regulation of ADP-glucose pyrophosphorylase is critical for the biosynthesis of glycogen in bacteria and starch in plants. The enzyme from Agrobacterium tumefaciens is activated by fructose 6-phosphate (Fru6P) and pyruvate (Pyr). The Pyr site has been recently found, but the site where Fru6P binds has remained unknown. We hypothesize that a sulfate ion previously found in the crystal structure reveals a part of the regulatory site mimicking the presence of the phosphoryl moiety of the activator Fru6P. Ser72 interacts with this sulfate ion and, if the hypothesis is correct, Ser72 would affect the interaction with Fru6P and activation of the enzyme. Here, we report structural, binding, and kinetic analysis of Ser72 mutants of the A. tumefaciens ADP-glucose pyrophosphorylase. By X-ray crystallography, we found that when Ser72 was replaced by Asp or Glu side chain carboxylates protruded into the sulfate-binding pocket. They would present a strong steric and electrostatic hindrance to the phosphoryl moiety of Fru6P, while being remote from the Pyr site. In agreement, we found that Fru6P could not activate or bind to S72E or S72D mutants, whereas Pyr was still an effective activator. These mutants also blocked the binding of the inhibitor AMP. This could potentially have biotechnological importance in obtaining enzyme forms insensitive to inhibition. Other mutations in this position (Ala, Cys, and Trp) confirmed the importance of Ser72 in regulation. We propose that the ADP-glucose pyrophosphorylase from A. tumefaciens have two distinct sites for Fru6P and Pyr working in tandem to regulate glycogen biosynthesis.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose-1-phosphate adenylyltransferase
A,
B,
C,
D,
E,
A,
B,
C,
D,
E,
F,
G,
H,
I,
J,
K,
L,
M,
N,
O,
P,
Q,
R,
T,
S [auth W]
440Agrobacterium fabrum str. C58Mutation(s): 1 
Gene Names: glgCAtu4076AGR_L_1560
EC: 2.7.7.27
UniProt
Find proteins for Q8U8L5 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore Q8U8L5 
Go to UniProtKB:  Q8U8L5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U8L5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B],
AB [auth E],
AC [auth I],
AD [auth M],
AE [auth Q],
AA [auth B],
AB [auth E],
AC [auth I],
AD [auth M],
AE [auth Q],
BA [auth B],
BB [auth E],
BC [auth I],
BD [auth N],
BE [auth Q],
CA [auth B],
CB [auth E],
CC [auth I],
CD [auth N],
CE [auth Q],
DA [auth B],
DB [auth F],
DC [auth J],
DD [auth N],
DE [auth Q],
EA [auth B],
EB [auth F],
EC [auth J],
ED [auth N],
EE [auth Q],
FA [auth B],
FB [auth F],
FC [auth J],
FD [auth N],
FE [auth Q],
GA [auth B],
GB [auth F],
GC [auth J],
GD [auth N],
GE [auth R],
HA [auth C],
HB [auth F],
HC [auth J],
HD [auth O],
HE [auth R],
IA [auth C],
IB [auth F],
IC [auth J],
ID [auth O],
IE [auth R],
JA [auth C],
JB [auth F],
JC [auth J],
JD [auth O],
JE [auth R],
KA [auth C],
KB [auth G],
KC [auth J],
KD [auth O],
KE [auth R],
LA [auth C],
LB [auth G],
LC [auth K],
LD [auth O],
LE [auth R],
MA [auth C],
MB [auth G],
MC [auth K],
MD [auth O],
ME [auth R],
NA [auth C],
NB [auth G],
NC [auth K],
ND [auth O],
NE [auth W],
OA [auth C],
OB [auth G],
OC [auth K],
OD [auth P],
OE [auth W],
PA [auth C],
PB [auth G],
PC [auth K],
PD [auth P],
PE [auth W],
QA [auth D],
QB [auth G],
QC [auth K],
QD [auth P],
QE [auth W],
RA [auth D],
RB [auth H],
RC [auth L],
RD [auth P],
RE [auth W],
SA [auth D],
SB [auth H],
SC [auth L],
SD [auth P],
SE [auth T],
TA [auth D],
TB [auth H],
TC [auth L],
TD [auth P],
TE [auth T],
U [auth A],
UA [auth D],
UB [auth H],
UC [auth L],
UD [auth P],
UE [auth T],
V [auth A],
VA [auth D],
VB [auth H],
VC [auth L],
VD [auth P],
VE [auth T],
W [auth A],
WA [auth E],
WB [auth I],
WC [auth L],
WD [auth P],
WE [auth T],
X [auth A],
XA [auth E],
XB [auth I],
XC [auth M],
XD [auth P],
XE [auth T],
Y [auth A],
YA [auth E],
YB [auth I],
YC [auth M],
YD [auth Q],
YE [auth T],
Z [auth A],
ZA [auth E],
ZB [auth I],
ZC [auth M],
ZD [auth Q],
ZE [auth T]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.416α = 108.067
b = 141.581β = 101.846
c = 228.316γ = 89.998
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Advisory, Database references