PDBsum entry 2rd5

Protein binding

PDB id: 2rd5

Contents

Protein chains

281 a.a. *

125 a.a. *

Ligands

ARG ×2

ADP ×2

NLG ×2

ATP ×2

Metals

_MG ×3

Waters ×64

* Residue conservation analysis

PDB id:

2rd5

Name:

Protein binding

Title:

Structural basis for the regulation of n-acetylglutamate kinase by pii in arabidopsis thaliana

Structure:

Acetylglutamate kinase-like protein. Chain: a, b. Engineered: yes. Pii protein. Chain: c, d. Synonym: p ii nitrogen sensing protein glb i, at4g01900. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: t8h10.160. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: at4g01900, t7b11.16.

Resolution:

2.51Å R-factor: 0.203 R-free: 0.229

Authors:

Y.Mizuno,G.B.G.Moorhead,K.K.S.Ng

Key ref:

Y.Mizuno et al. (2007). Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana. J Biol Chem, 282, 35733-35740. PubMed id: 17913711 DOI: 10.1074/jbc.M707127200

Date:

21-Sep-07 Release date: 02-Oct-07

Protein chains

Q9SCL7  (NAGK_ARATH) -  Acetylglutamate kinase, chloroplastic from Arabidopsis thaliana

Seq: 347 a.a.

Struc: 281 a.a.

Protein chains

Q9ZST4  (GLNB_ARATH) -  Nitrogen regulatory protein P-II homolog from Arabidopsis thaliana

Seq: 196 a.a.

Struc: 125 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.2.7.2.8 - acetylglutamate kinase.
• Pathway: Ornithine Biosynthesis
• Reaction: N-acetyl-L-glutamate + ATP = N-acetyl-L-glutamyl 5-phosphate + ADP

N-acetyl-L-glutamate (Bound ligand (Het Group name = ATP) corresponds exactly) + ATP (Bound ligand (Het Group name = NLG) corresponds exactly) = N-acetyl-L-glutamyl 5-phosphate (Bound ligand (Het Group name = ADP) corresponds exactly) + ADP

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

reference

DOI no: 10.1074/jbc.M707127200

J Biol Chem 282:35733-35740 (2007)

PubMed id: 17913711

Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana.

Y.Mizuno, G.B.Moorhead, K.K.Ng.

ABSTRACT

PII is a highly conserved regulatory protein found in organisms across the three domains of life. In cyanobacteria and plants, PII relieves the feedback inhibition of the rate-limiting step in arginine biosynthesis catalyzed by N-acetylglutamate kinase (NAGK). To understand the molecular structural basis of enzyme regulation by PII, we have determined a 2.5-A resolution crystal structure of a complex formed between two homotrimers of PII and a single hexamer of NAGK from Arabidopsis thaliana bound to the metabolites N-acetylglutamate, ADP, ATP, and arginine. In PII, the T-loop and Trp(22) at the start of the alpha1-helix, which are both adjacent to the ATP-binding site of PII, contact two beta-strands as well as the ends of two central helices (alphaE and alphaG) in NAGK, the opposing ends of which form major portions of the ATP and N-acetylglutamate substrate-binding sites. The binding of Mg(2+).ATP to PII stabilizes a conformation of the T-loop that favors interactions with both open and closed conformations of NAGK. Interactions between PII and NAGK appear to limit the degree of opening and closing of the active-site cleft in opposition to a domain-separating inhibitory effect exerted by arginine, thus explaining the stimulatory effect of PII on the kinetics of arginine-inhibited NAGK.

Selected figure(s)

Figure 1.
Overall structure of the PII·NAGK complex.A and B, top and bottom views, respectively, along the molecular 3-fold rotational axis; C, side view along the 2-fold axis bisecting interface A; D, side view along the 2-fold axis bisecting interface B. In A and B, the views taken in C and D are marked with gray letters beside the respective 2-fold rotational axes. In C and D, the views taken in A and B are marked with gray letters beside the 3-fold rotational axis. PII is colored dark gray; ATP bound to PII and ADP bound to NAGK are colored magenta. NAGK protomers are colored yellow and green; N-acetylglutamate (NAG) is colored red, and arginine is colored blue. Figs. 1, 2, 3, 4 were prepared using PyMOL (38).

Figure 4.
Open and closed conformations of NAGK drawn as α-carbon traces. Shown are the open (A) and closed (B) conformations of A. thaliana NAGK and the open conformation of T. maritima NAGK bound to arginine (C) (21). ADP and N-acetylglutamate (NAG) are drawn in stick representation. The N-terminal domain (N-term; residues 15-211) is colored blue, and the C-terminal domain (C-term; residues 212-297) is colored red. The black dot marks the position of the rotational axis that is normal to the plane of the page. Rotating the N-terminal domain of the open form of NAGK by 11° about this axis in the direction indicated by the arrow in A would result in the closed conformation shown in B. The right panels show a “top” view similar to that used in Fig. 2A. This view is perpendicular to the rotational axis, which is drawn as a light gray arrow.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 35733-35740) copyright 2007.

Figures were selected by an automated process.