3MUM

Crystal Structure of the G20A mutant c-di-GMP riboswith bound to c-di-GMP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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Literature

Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch .

Smith, K.D., Lipchock, S.V., Livingston, A.L., Shanahan, C.A., Strobel, S.A.

(2010) Biochemistry 49: 7351-7359

  • DOI: https://doi.org/10.1021/bi100671e
  • Primary Citation of Related Structures:  
    3MUM, 3MUR, 3MUT, 3MUV, 3MXH

  • PubMed Abstract: 

    • The bacterial second messenger c-di-GMP is used in many species to control essential processes that allow the organism to adapt to its environment. The c-di-GMP riboswitch (GEMM) is an important downstream target in this signaling pathway and alters gene expression in response to changing concentrations of c-di-GMP ...

    The bacterial second messenger c-di-GMP is used in many species to control essential processes that allow the organism to adapt to its environment. The c-di-GMP riboswitch (GEMM) is an important downstream target in this signaling pathway and alters gene expression in response to changing concentrations of c-di-GMP. The riboswitch selectively recognizes its second messenger ligand primarily through contacts with two critical nucleotides. However, these two nucleotides are not the most highly conserved residues within the riboswitch sequence. Instead, nucleotides that stack with c-di-GMP and that form tertiary RNA contacts are the most invariant. Biochemical and structural evidence reveals that the most common natural variants are able to make alternative pairing interactions with both guanine bases of the ligand. Additionally, a high-resolution (2.3 A) crystal structure of the native complex reveals that a single metal coordinates the c-di-GMP backbone. Evidence is also provided that after transcription of the first nucleotide on the 3'-side of the P1 helix, which is predicted to be the molecular switch, the aptamer is functional for ligand binding. Although large energetic effects occur when several residues in the RNA are altered, mutations at the most conserved positions, rather than at positions that base pair with c-di-GMP, have the most detrimental effects on binding. Many mutants retain sufficient c-di-GMP affinity for the RNA to remain biologically relevant, which suggests that this motif is quite resilient to mutation.

    Organizational Affiliation: 

    Department of Chemistry, Yale University, New Haven,Connecticut 06520, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein AA [auth P]98Homo sapiensMutation(s): 2 
Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09012
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
G20A mutant c-di-GMP RiboswitchB [auth R]92N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E
Download Ideal Coordinates CCD File 
C [auth R]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
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth R],
E [auth R]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
C2E PDBBind:  3MUM Kd: 0.21 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.115α = 90
b = 45.596β = 93.99
c = 79.821γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-06
    Changes: Database references, Derived calculations, Structure summary