Crystal structure of universal stress protein MSMEG_3811 in complex with cAMP

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

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A Universal Stress Protein (Usp) in Mycobacteria Binds Camp

Banerjee, A.Adolph, R.S.Gopalakrishnapai, J.Kleinboelting, S.Emmerich, C.Steegborn, C.Visweswariah, S.S.

(2015) J Biol Chem 290: 12731

  • DOI: https://doi.org/10.1074/jbc.M115.644856
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Mycobacteria are endowed with rich and diverse machinery for the synthesis, utilization, and degradation of cAMP. The actions of cyclic nucleotides are generally mediated by binding of cAMP to conserved and well characterized cyclic nucleotide binding domains or structurally distinct cGMP-specific and -regulated cyclic nucleotide phosphodiesterase, adenylyl cyclase, and E. coli transcription factor FhlA (GAF) domain-containing proteins. Proteins with cyclic nucleotide binding and GAF domains can be identified in the genome of mycobacterial species, and some of them have been characterized. Here, we show that a significant fraction of intracellular cAMP is bound to protein in mycobacterial species, and by using affinity chromatography techniques, we identify specific universal stress proteins (USP) as abundantly expressed cAMP-binding proteins in slow growing as well as fast growing mycobacteria. We have characterized the biochemical and thermodynamic parameters for binding of cAMP, and we show that these USPs bind cAMP with a higher affinity than ATP, an established ligand for other USPs. We determined the structure of the USP MSMEG_3811 bound to cAMP, and we confirmed through structure-guided mutagenesis, the residues important for cAMP binding. This family of USPs is conserved in all mycobacteria, and we suggest that they serve as "sinks" for cAMP, making this second messenger available for downstream effectors as and when ATP levels are altered in the cell.

  • Organizational Affiliation

    From the Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Find proteins for A0QYW6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QYW6 
Go to UniProtKB:  A0QYW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QYW6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on POG

Download Ideal Coordinates CCD File 
O [auth C],
S [auth D],
X [auth F]
C21 H44 O8
Query on CMP

Download Ideal Coordinates CCD File 
G [auth A]
K [auth B]
N [auth C]
P [auth D]
T [auth E]
G [auth A],
K [auth B],
N [auth C],
P [auth D],
T [auth E],
U [auth F]
C10 H12 N5 O6 P
Query on SO4

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H [auth A]
I [auth A]
L [auth B]
Q [auth D]
R [auth D]
H [auth A],
I [auth A],
L [auth B],
Q [auth D],
R [auth D],
V [auth F],
W [auth F]
O4 S
Query on CL

Download Ideal Coordinates CCD File 
J [auth A],
M [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
CMP Binding MOAD:  5AHW Kd: 64 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.53α = 90
b = 126.78β = 90
c = 151.72γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Database references
  • Version 1.2: 2015-06-03
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary