PDBsum entry: 1w25

Signaling protein

PDB id: 1w25

Contents

Protein chains

454 a.a. *

Ligands

C2E ×5

Metals

_ZN

_MG ×2

Waters ×15

* Residue conservation analysis

PDB id:

1w25

Name:

Signaling protein

Title:

Response regulator pled in complex with c-digmp

Structure:

Stalked-cell differentiation controlling protein. Chain: a, b. Synonym: diguanylate cyclase. Engineered: yes

Source:

Caulobacter vibrioides. Organism_taxid: 190650. Strain: cb15. Atcc: 19089. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.70Å R-factor: 0.212 R-free: 0.239

Authors:

C.Chan,T.Schirmer,U.Jenal

Key ref:

C.Chan et al. (2004). Structural basis of activity and allosteric control of diguanylate cyclase. Proc Natl Acad Sci U S A, 101, 17084-17089. PubMed id: 15569936 DOI: 10.1073/pnas.0406134101

Date:

28-Jun-04 Release date: 18-Nov-04

Protein chains

B8GZM2  (PLED_CAUCN) -  Response regulator PleD

Seq: 454 a.a.

Struc: 454 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.65 - Diguanylate cyclase.
• Reaction: 2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate

2 × GTP = 2 × diphosphate + cyclic di-3',5'-guanylate (Bound ligand (Het Group name = C2E) corresponds exactly)

• Cofactor: Magnesium; Manganese

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: intracellular signal transduction (7 terms)
• Biochemical function: diguanylate cyclase activity (8 terms)

reference

DOI no: 10.1073/pnas.0406134101

Proc Natl Acad Sci U S A 101:17084-17089 (2004)

PubMed id: 15569936

Structural basis of activity and allosteric control of diguanylate cyclase.

C.Chan, R.Paul, D.Samoray, N.C.Amiot, B.Giese, U.Jenal, T.Schirmer.

ABSTRACT

Recent discoveries suggest that a novel second messenger, bis-(3'-->5')-cyclic di-GMP (c-diGMP), is extensively used by bacteria to control multicellular behavior. Condensation of two GTP to the dinucleotide is catalyzed by the widely distributed diguanylate cyclase (DGC or GGDEF) domain that occurs in various combinations with sensory and/or regulatory modules. The crystal structure of the unorthodox response regulator PleD from Caulobacter crescentus, which consists of two CheY-like receiver domains and a DGC domain, has been solved in complex with the product c-diGMP. PleD forms a dimer with the CheY-like domains (the stem) mediating weak monomer-monomer interactions. The fold of the DGC domain is similar to adenylate cyclase, but the nucleotide-binding mode is substantially different. The guanine base is H-bonded to Asn-335 and Asp-344, whereas the ribosyl and alpha-phosphate moieties extend over the beta2-beta3-hairpin that carries the GGEEF signature motif. In the crystal, c-diGMP molecules are crosslinking active sites of adjacent dimers. It is inferred that, in solution, the two DGC domains of a dimer align in a two-fold symmetric way to catalyze c-diGMP synthesis. Two mutually intercalated c-diGMP molecules are found tightly bound at the stem-DGC interface. This allosteric site explains the observed noncompetitive product inhibition. We propose that product inhibition is due to domain immobilization and sets an upper limit for the concentration of this second messenger in the cell.

Selected figure(s)

Figure 3.
Fig. 3. Product binding to the allosteric inhibitory I-site. (a) A close-up view of the two mutually intercalated c-diGMP molecules (khaki and gray carbon atoms) bound at the D2 (yellow)-DGC (green) interface. The omit map of the ligand is contoured at 4 .(b) The ligand is tightly bound to both domains [carbons are colored in magenta (D2) and cyan (DGC)] by a multitude of specific interactions, including a recurrent arginine-guanine-binding motif. Figures were generated by DINO (A. Philippsen, www.dino3d.org).

Figure 4.
Fig. 4. Mechanistic model of PleD regulation. The catalytic DGC domain (green) is tethered via a flexible linker peptide to the D1/D2 stem. The DGC domain is postulated to be mobile with respect to the stem, as indicated by the curved broken arrow. (Upper) PleD is activated by phosphorylation at the D1 domain, which induces dimerization mediated by the stems and allows the two substrate-binding sites (with bound GTP substrate in yellow) to approach each other and the condensation reaction (2 GTP c-diGMP + 2 PPi) to occur. (Lower) Allosteric product inhibition occurs by binding of (c-diGMP)[2] to the I-site at the stem-DGC interface, whereby the DGC domain is immobilized with respect to the stem and barred from approaching its counterpart in the dimer.

Figures were selected by an automated process.