Lcd1 GAF domain in complex with cAMP ligand

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structural and Enzymatic Characterization of a cAMP-Dependent Diguanylate Cyclase from Pathogenic Leptospira Species.

da Costa Vasconcelos, F.N.Maciel, N.K.Favaro, D.C.de Oliveira, L.C.Barbosa, A.S.Salinas, R.K.de Souza, R.F.Farah, C.S.Guzzo, C.R.

(2017) J Mol Biol 429: 2337-2352

  • DOI: https://doi.org/10.1016/j.jmb.2017.06.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Leptospira interrogans serovar Copenhageni is a human pathogen that causes leptospirosis, a worldwide zoonosis. The L. interrogans genome codes for a wide array of potential diguanylate cyclase (DGC) enzymes with characteristic GGDEF domains capable of synthesizing the cyclic dinucleotide c-di-GMP, known to regulate transitions between different cellular behavioral states in bacteria. Among such enzymes, LIC13137 (Lcd1), which has an N-terminal cGMP-specific phosphodiesterases, adenylyl cyclases, and FhlA (GAF) domain and a C-terminal GGDEF domain, is notable for having close orthologs present only in pathogenic Leptospira species. Although the function and structure of GGDEF and GAF domains have been studied extensively separately, little is known about enzymes with the GAF-GGDEF architecture. In this report, we address the question of how the GAF domain regulates the DGC activity of Lcd1. The full-length Lcd1 and its GAF domain form dimers in solution. The GAF domain binds specifically cAMP (K D of 0.24μM) and has an important role in the regulation of the DGC activity of the GGDEF domain. Lcd1 DGC activity is negligible in the absence of cAMP and is significantly enhanced in its presence (specific activity of 0.13s -1 ). The crystal structure of the Lcd1 GAF domain in complex with cAMP provides valuable insights toward explaining its specificity for cAMP and pointing to possible mechanisms by which this cyclic nucleotide regulates the assembly of an active DGC enzyme.

  • Organizational Affiliation

    Departamento de Microbiologia, Instituto de Ciências Biomedicas, Universidade de São Paulo, São Paulo, 05508-900, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-specific phosphodiesterase
A, B, C, D
195Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130Mutation(s): 0 
Gene Names: LIC_13137
Find proteins for Q72MQ6 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130))
Explore Q72MQ6 
Go to UniProtKB:  Q72MQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72MQ6
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D
Binding Affinity Annotations 
IDSourceBinding Affinity
CMP Binding MOAD:  5W10 Kd: 240 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.19α = 90
b = 119.995β = 90
c = 62.454γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2016/084147
Sao Paulo Research Foundation (FAPESP)Brazil2013/18664-2
Sao Paulo Research Foundation (FAPESP)Brazil2013/06650-7
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil474907/2013-9

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence