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 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

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Ligand Structure Quality Assessment 

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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: https://doi.org/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 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diguanylate cyclase177Marinobacter nauticus VT8Mutation(s): 0 
Gene Names: Maqu_2607
EC: 2.7.7.65
UniProt
Find proteins for A1U3W3 (Marinobacter nauticus (strain ATCC 700491 / DSM 11845 / VT8))
Explore A1U3W3 
Go to UniProtKB:  A1U3W3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1U3W3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E

Download Ideal Coordinates CCD File 
B [auth A],
C [auth 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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free:  0.240 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted C2EClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary