3IGN

Crystal Structure of the GGDEF domain from Marinobacter aquaeolei diguanylate cyclase complexed with c-di-GMP - Northeast Structural Genomics Consortium Target MqR89a

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of a catalytically active GG(D/E)EF diguanylate cyclase domain from Marinobacter aquaeolei with bound c-di-GMP product.

Vorobiev, S.M., Neely, H., Yu, B., Seetharaman, J., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F.

(2012) J Struct Funct Genomics 13: 177-183

  • DOI: 10.1007/s10969-012-9136-4
  • Primary Citation of Related Structures:  
    3IGN

  • PubMed Abstract: 

    • Recent studies of signal transduction in bacteria have revealed a unique second messenger, bis-(3'-5')-cyclic dimeric GMP (c-di-GMP), which regulates transitions between motile states and sessile states, such as biofilms. C-di-GMP is synthesized from ...

    Recent studies of signal transduction in bacteria have revealed a unique second messenger, bis-(3'-5')-cyclic dimeric GMP (c-di-GMP), which regulates transitions between motile states and sessile states, such as biofilms. C-di-GMP is synthesized from two GTP molecules by diguanylate cyclases (DGC). The catalytic activity of DGCs depends on a conserved GG(D/E)EF domain, usually part of a larger multi-domain protein organization. The domains other than the GG(D/E)EF domain often control DGC activation. This paper presents the 1.83 Å crystal structure of an isolated catalytically competent GG(D/E)EF domain from the A1U3W3_MARAV protein from Marinobacter aquaeolei. Co-crystallization with GTP resulted in enzymatic synthesis of c-di-GMP. Comparison with previously solved DGC structures shows a similar orientation of c-di-GMP bound to an allosteric regulatory site mediating feedback inhibition of the enzyme. Biosynthesis of c-di-GMP in the crystallization reaction establishes that the enzymatic activity of this DGC domain does not require interaction with regulatory domains.

    Organizational Affiliation: 

    Department of Biological Sciences, The Northeast Structural Genomics Consortium Columbia University, New York, NY, 10032, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Diguanylate cyclaseA177Marinobacter hydrocarbonoclasticus VT8Mutation(s): 0 
Gene Names: Maqu_2607
EC: 2.7.7.65
Find proteins for A1U3W3 (Marinobacter hydrocarbonoclasticus (strain ATCC 700491 / DSM 11845 / VT8))
Explore A1U3W3 
Go to UniProtKB:  A1U3W3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E
Download Ideal Coordinates CCD File 
A
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.229α = 90
b = 59.229β = 90
c = 118.895γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SnBphasing
RESOLVEmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2016-05-11
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description