PDBsum entry 2v5h

Transcription

PDB id: 2v5h

Contents

Protein chains

(+ 0 more) 284 a.a. *

(+ 0 more) 111 a.a. *

Ligands

NLG ×6

GOL

Metals

_NA ×6

_CL ×6

Waters ×187

* Residue conservation analysis

PDB id:

2v5h

Name:

Transcription

Title:

Controlling the storage of nitrogen as arginine: the complex of pii and acetylglutamate kinase from synechococcus elongatus pcc 7942

Structure:

Acetylglutamate kinase. Chain: a, b, c, d, e, f. Synonym: NAG kinase, agk, n-acetyl-l-glutamate 5-phosphotransferase. Engineered: yes. Nitrogen regulatory protein p-ii. Chain: g, h, i, j, k, l. Synonym: pii protein, pii signal transducing protein. Engineered: yes

Source:

Synechococcus elongatus. Organism_taxid: 1140. Strain: pcc 7942. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.75Å R-factor: 0.202 R-free: 0.236

Authors:

J.L.Llacer,C.Marco-Marin,F.Gil-Ortiz,I.Fita,V.Rubio

Key ref:

J.L.Llácer et al. (2007). The crystal structure of the complex of PII and acetylglutamate kinase reveals how PII controls the storage of nitrogen as arginine. Proc Natl Acad Sci U S A, 104, 17644-17649. PubMed id: 17959776 DOI: 10.1073/pnas.0705987104

Date:

04-Jul-07 Release date: 16-Oct-07

Protein chains

Q6V1L5  (ARGB_SYNE7) -  Acetylglutamate kinase from Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)

Seq: 301 a.a.

Struc: 284 a.a.

Protein chains

P0A3F4  (GLNB_SYNE7) -  Nitrogen regulatory protein P-II from Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)

Seq: 112 a.a.

Struc: 111 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F: 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 + ATP (Bound ligand (Het Group name = NLG) corresponds exactly) = N-acetyl-L-glutamyl 5-phosphate + ADP

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

reference

DOI no: 10.1073/pnas.0705987104

Proc Natl Acad Sci U S A 104:17644-17649 (2007)

PubMed id: 17959776

The crystal structure of the complex of PII and acetylglutamate kinase reveals how PII controls the storage of nitrogen as arginine.

J.L.Llácer, A.Contreras, K.Forchhammer, C.Marco-Marín, F.Gil-Ortiz, R.Maldonado, I.Fita, V.Rubio.

ABSTRACT

Photosynthetic organisms can store nitrogen by synthesizing arginine, and, therefore, feedback inhibition of arginine synthesis must be relieved in these organisms when nitrogen is abundant. This relief is accomplished by the binding of the PII signal transduction protein to acetylglutamate kinase (NAGK), the controlling enzyme of arginine synthesis. Here, we describe the crystal structure of the complex between NAGK and PII of Synechococcus elongatus, at 2.75-A resolution. We prove the physiological relevance of the observed interactions by site-directed mutagenesis and functional studies. The complex consists of two polar PII trimers sandwiching one ring-like hexameric NAGK (a trimer of dimers) with the threefold axes of these molecules aligned. The binding of PII favors a narrow ring conformation of the NAGK hexamer that is associated with arginine sites having low affinity for this inhibitor. Each PII subunit contacts one NAGK subunit only. The contacts map in the inner circumference of the NAGK ring and involve two surfaces of the PII subunit. One surface is on the PII body and interacts with the C-domain of the NAGK subunit, helping widen the arginine site found on the other side of this domain. The other surface is at the distal region of a protruding large loop (T-loop) that presents a novel compact shape. This loop is inserted in the interdomain crevice of the NAGK subunit, contacting mainly the N-domain, and playing key roles in anchoring PII on NAGK, in activating NAGK, and in complex formation regulation by MgATP, ADP, 2-oxoglutarate, and by phosphorylation of serine-49.

Selected figure(s)

Figure 1.
Fig. 1. P[II]–NAGK complex. NAGK, P[II], and NAG are shown as surface, ribbons, and spheres, respectively. NAGK dimers and P[II] subunits are colored independently. Views are along the threefold axis (A) or the twofold axis (B).

Figure 2.
Fig. 2. P[II] subunit–NAGK subunit contacts. P[II], NAGK, and NAG are shown as strings, ribbons, and spheres, respectively. The contacting parts of the T-loop, B-loop, and 1– 1 connection, including some interacting side chains (in sticks), are blue, red, and green, respectively. The surfaces provided by these elements form meshworks of the same colors. The NAGK central -sheet is green, and other -strands and the -helices are brownish and grayish for N- and C-domains, respectively. Some NAGK elements and P[II] residues are labeled. (Inset) Structure of bound NAG, encased within its electron density omit map contoured at 2.5 .

Figures were selected by an automated process.