PDBsum entry 2d3b

Ligase

PDB id: 2d3b

Contents

Protein chains

(+ 4 more) 353 a.a. *

Ligands

ANP ×10

MSL ×10

Metals

_MN ×30

Waters ×377

* Residue conservation analysis

PDB id:

2d3b

Name:

Ligase

Title:

Crystal structure of the maize glutamine synthetase complexed with amppnp and methionine sulfoximine

Structure:

Glutamine synthetase. Chain: a, b, c, d, e, f, g, h, i, j. Engineered: yes

Source:

Zea mays. Organism_taxid: 4577. Gene: gs1a. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Decamer (from PQS)

Resolution:

3.50Å R-factor: 0.168 R-free: 0.209

Authors:

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

Key ref:

H.Unno et al. (2006). Atomic structure of plant glutamine synthetase: a key enzyme for plant productivity. J Biol Chem, 281, 29287-29296. PubMed id: 16829528 DOI: 10.1074/jbc.M601497200

Date:

26-Sep-05 Release date: 18-Jul-06

Protein chains

P38561  (GLNA3_MAIZE) -  Glutamine synthetase root isozyme 3 from Zea mays

Seq: 356 a.a.

Struc: 353 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.6.3.1.2 - glutamine synthetase.
• Reaction: L-glutamate + NH4⁺ + ATP = L-glutamine + ADP + phosphate + H⁺

L-glutamate + NH4(+) (Bound ligand (Het Group name = MSL) matches with 50.00% similarity) + ATP = L-glutamine (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + ADP + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M601497200

J Biol Chem 281:29287-29296 (2006)

PubMed id: 16829528

Atomic structure of plant glutamine synthetase: a key enzyme for plant productivity.

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

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. 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.

Selected figure(s)

Figure 4.
FIGURE 4. Representation of the interactions between enzyme and substrate analogues. a, stick models for the interaction of the enzyme with AMPPNP and MetSox. Carbon, oxygen, nitrogen, phosphorus, and sulfur atoms are colored gray, red, blue, salmon, and yellow, respectively. Three Mn^2+ are indicated in pink spheres. Dotted lines designate hydrogen bonds and coordination bonds to Mn^2+ ions. Residues without dotted lines have hydrophobic interactions with the substrate. b, stick models for the interaction of the enzyme with ADP and MetSox. c, stick models for the interaction of the enzyme with ADP and PPT-P.

Figure 7.
FIGURE 7. Active site structure formed by Asp-56 and Glu-297 of maize GS1a. a, stereo view of the side chain structures of Asp-56' and Glu-297 together with ADP, MetSox-P, and three Mn^2+ ions. b, alignments of short stretches of amino acid sequences containing Asp-56 and Glu-297 in GSs from M. tuberculosis (MtGS), S. typhimurium (StGS), maize (GS1 isozymes GS1a, GS1d, andGS2), Arabidopsis, human, and chicken.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 29287-29296) copyright 2006.

Figures were selected by an automated process.