2D3A

Crystal Structure of the Maize Glutamine Synthetase complexed with ADP and Methionine sulfoximine Phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Atomic Structure of Plant Glutamine Synthetase: A KEY ENZYME FOR PLANT PRODUCTIVITY

Unno, H.Uchida, T.Sugawara, H.Kurisu, G.Sugiyama, T.Yamaya, T.Sakakibara, H.Hase, T.Kusunoki, M.

(2006) J Biol Chem 281: 29287-29296

  • DOI: 10.1074/jbc.M601497200
  • Primary Citation of Related Structures:  
    2D3A, 2D3B, 2D3C

  • PubMed Abstract: 
  • Plants provide nourishment for animals and other heterotrophs as the sole primary producer in the food chain. Glutamine synthetase (GS), one of the essential enzymes for plant autotrophy catalyzes the incorporation of ammonia into glutamate to generate glutamine with concomitant hydrolysis of ATP, and plays a crucial role in the assimilation and re-assimilation of ammonia derived from a wide variety of metabolic processes during plant growth and development ...

    Plants provide nourishment for animals and other heterotrophs as the sole primary producer in the food chain. Glutamine synthetase (GS), one of the essential enzymes for plant autotrophy catalyzes the incorporation of ammonia into glutamate to generate glutamine with concomitant hydrolysis of ATP, and plays a crucial role in the assimilation and re-assimilation of ammonia derived from a wide variety of metabolic processes during plant growth and development. Elucidation of the atomic structure of higher plant GS is important to understand its detailed reaction mechanism and to obtain further insight into plant productivity and agronomical utility. Here we report the first crystal structures of maize (Zea mays L.) GS. The structure reveals a unique decameric structure that differs significantly from the bacterial GS structure. Higher plants have several isoenzymes of GS differing in heat stability and catalytic properties for efficient responses to variation in the environment and nutrition. A key residue responsible for the heat stability was found to be Ile-161 in GS1a. The three structures in complex with substrate analogues, including phosphinothricin, a widely used herbicide, lead us to propose a mechanism for the transfer of phosphate from ATP to glutamate and to interpret the inhibitory action of phosphinothricin as a guide for the development of new potential herbicides.


    Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
glutamine synthetase
A, B, C, D, E, F, G, H, I, J
A, B, C, D, E, F, G, H, I, J
356Zea maysMutation(s): 0 
Gene Names: gs1aGLN4GS1-3
EC: 6.3.1.2
UniProt
Find proteins for P38561 (Zea mays)
Explore P38561 
Go to UniProtKB:  P38561
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38561
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
CB [auth I],
DA [auth D],
HB [auth J],
IA [auth E],
NA [auth F],
CB [auth I],
DA [auth D],
HB [auth J],
IA [auth E],
NA [auth F],
O [auth A],
SA [auth G],
T [auth B],
XA [auth H],
Y [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
P3S
Query on P3S

Download Ideal Coordinates CCD File 
BB [auth I],
CA [auth D],
GB [auth J],
HA [auth E],
MA [auth F],
BB [auth I],
CA [auth D],
GB [auth J],
HA [auth E],
MA [auth F],
N [auth A],
RA [auth G],
S [auth B],
WA [auth H],
X [auth C]
L-METHIONINE-S-SULFOXIMINE PHOSPHATE
C5 H13 N2 O6 P S
QQFOFBSCSWFFPB-NMAPHRJESA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth D],
AB [auth I],
BA [auth D],
DB [auth J],
EA [auth E],
AA [auth D],
AB [auth I],
BA [auth D],
DB [auth J],
EA [auth E],
EB [auth J],
FA [auth E],
FB [auth J],
GA [auth E],
JA [auth F],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
M [auth A],
OA [auth G],
P [auth B],
PA [auth G],
Q [auth B],
QA [auth G],
R [auth B],
TA [auth H],
U [auth C],
UA [auth H],
V [auth C],
VA [auth H],
W [auth C],
YA [auth I],
Z [auth D],
ZA [auth I]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.795α = 90
b = 191.041β = 101.47
c = 118.103γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance