PDBsum entry 2v0n

Lyase

PDB id: 2v0n

Contents

Protein chains

459 a.a. *

Ligands

BEF ×2

C2E ×4

GAV ×2

SO4 ×2

Metals

_CL

_MG ×5

Waters ×14

* Residue conservation analysis

PDB id:

2v0n

Name:

Lyase

Title:

Activated response regulator pled in complex with c-digmp and gtp- alpha-s

Structure:

Response regulator pled. Chain: a, b. Fragment: residues 2-454. Synonym: stalked cell differentiation-controlling protein, pled. Engineered: yes. Other_details: berrylium fluoride modification of a 53 and b 53

Source:

Caulobacter vibrioides. Organism_taxid: 190650. Strain: cb15. Atcc: 19089. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: plyss.

Resolution:

2.71Å R-factor: 0.216 R-free: 0.252

Authors:

P.Wassmann,T.Schirmer

Key ref:

P.Wassmann et al. (2007). Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition. Structure, 15, 915-927. PubMed id: 17697997 DOI: 10.1016/j.str.2007.06.016

Date:

15-May-07 Release date: 21-Aug-07

Protein chains

B8GZM2  (PLED_CAUVN) -  Response regulator PleD from Caulobacter vibrioides (strain NA1000 / CB15N)

Seq: 454 a.a.

Struc: 459 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.65 - diguanylate cyclase.
• Reaction: 2 GTP = 3',3'-c-di-GMP + 2 diphosphate

2 × GTP (Bound ligand (Het Group name = GAV) matches with 93.94% similarity) = 3',3'-c-di-GMP + 2 × diphosphate

• Cofactor: Mg(2+); Mn(2+)

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

Added reference

DOI no: 10.1016/j.str.2007.06.016

Structure 15:915-927 (2007)

PubMed id: 17697997

Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition.

P.Wassmann, C.Chan, R.Paul, A.Beck, H.Heerklotz, U.Jenal, T.Schirmer.

ABSTRACT

Cyclic di-guanosine monophosphate (c-di-GMP) is a ubiquitous bacterial second messenger involved in the regulation of cell surface-associated traits and persistence. We have determined the crystal structure of PleD from Caulobacter crescentus, a response regulator with a diguanylate cyclase (DGC) domain, in its activated form. The BeF(3)(-) modification of its receiver domain causes rearrangement with respect to an adaptor domain, which, in turn, promotes dimer formation, allowing for the efficient encounter of two symmetric catalytic domains. The substrate analog GTPalphaS and two putative cations are bound to the active sites in a manner similar to adenylate cyclases, suggesting an analogous two-metal catalytic mechanism. An allosteric c-di-GMP-binding mode that crosslinks DGC and an adaptor domain had been identified before. Here, a second mode is observed that crosslinks the DGC domains within a PleD dimer. Both modes cause noncompetitive product inhibition by domain immobilization.

Selected figure(s)

Figure 5.
Figure 5. Substrate Analog GTPαS and Mg^2+ Bound to the Active Site of PleD
The omit map for the ligands is contoured at 3σ. The DGC domain is shown in ribbon representation; the GGEEF signature hairpin is shown in dark blue, and all interacting residues and the P loop main chain (residues 328–331) are shown in full. (c-di-GMP)[2] bound to the I[p] site of the DGC domain can be seen in the rear.

Figure 6.
Figure 6. Crosslinking of the DGC Domains by c-di-GMP
(A) Ribbon diagram of the DGC dimer along its symmetry axis; both (c-di-GMP)[2] ligands and interacting residues are shown in full. The (c-di-GMP)[2] ligands are bound to the I site (I[P] site and the I[s,DGC] site of the adjacent subunit).
(B) Close-up view of the intercalated (c-di-GMP)[2] ligand, which crosslinks the two DGC domains (dark- and light-green surface representation) by binding to the I[p] (Arg359, Asp362, Arg390) and the I[s,DGC] (R313′) site of the adjacent domain.

The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 915-927) copyright 2007.

Figures were selected by an automated process.