3IB8

Crystal structure of full length Rv0805 in complex with 5'-AMP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

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This is version 1.2 of the entry. See complete history. 


Literature

A mycobacterial cyclic AMP phosphodiesterase that moonlights as a modifier of cell wall permeability

Podobnik, M., Tyagi, R., Matange, N., Dermol, U., Gupta, A.K., Mattoo, R., Seshadri, K., Visweswariah, S.S.

(2009) J Biol Chem 284: 32846-32857

  • DOI: 10.1074/jbc.M109.049635
  • Primary Citation of Related Structures:  
    3IB7, 3IB8

  • PubMed Abstract: 

    • Mycobacterium tuberculosis utilizes many mechanisms to establish itself within the macrophage, and bacterially derived cAMP is important in modulating the host cellular response. Although the genome of M. tuberculosis is endowed with a number of mammalian-like adenylyl cyclases, only a single cAMP phosphodiesterase has been identified that can decrease levels of cAMP produced by the bacterium ...

    Mycobacterium tuberculosis utilizes many mechanisms to establish itself within the macrophage, and bacterially derived cAMP is important in modulating the host cellular response. Although the genome of M. tuberculosis is endowed with a number of mammalian-like adenylyl cyclases, only a single cAMP phosphodiesterase has been identified that can decrease levels of cAMP produced by the bacterium. We present the crystal structure of the full-length and sole cAMP phosphodiesterase, Rv0805, found in M. tuberculosis, whose orthologs are present only in the genomes of slow growing and pathogenic mycobacteria. The dimeric core catalytic domain of Rv0805 adopts a metallophosphoesterase-fold, and the C-terminal region builds the active site and contributes to multiple substrate utilization. Localization of Rv0805 to the cell wall is dependent on its C terminus, and expression of either wild type or mutationally inactivated Rv0805 in M. smegmatis alters cell permeability to hydrophobic cytotoxic compounds. Rv0805 may therefore play a key role in the pathogenicity of mycobacteria, not only by hydrolyzing bacterial cAMP, but also by moonlighting as a protein that can alter cell wall functioning.

    Related Citations: 
    • Structural and biochemical analysis of the Rv0805 cyclic nucleotide phosphodiesterase from Mycobacterium tuberculosis
      Shenoy, A.R., Capuder, M., Draskovic, P., Lamba, D., Visweswariah, S.S., Podobnik, M.
      (2007) J Mol Biol 365: 211
    • The Rv0805 gene from Mycobacterium tuberculosis encodes a 3',5'-cyclic nucleotide phosphodiesterase: biochemical and mutational analysis
      Shenoy, A.R., Sreenath, N., Podobnik, M., Kovacevic, M., Visweswariah, S.S.
      (2005) Biochemistry 44: 15695
    Organizational Affiliation: 

    Laboratory for Biosynthesis and Biotransformation, National Institute of Chemistry of Slovenia, Hajdrihova 19,1000 Ljubljana, Slovenia. marjetka.podobnik@ki.si



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Icc proteinA330Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv0805
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
UniProt
Find proteins for P9WP65 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WP65 
Go to UniProtKB:  P9WP65
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WP65
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP
Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N		 Ligand Interaction
BTB
Query on BTB
Download Ideal Coordinates CCD File 
E [auth A]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N		 Ligand Interaction
MPD
Query on MPD
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]		(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
I [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
FE
Query on FE
Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.4α = 90
b = 100.4β = 90
c = 80.801γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description