PMID- 19898477
OWN - NLM
STAT- MEDLINE
DCOM- 20091230
LR  - 20211020
IS  - 1545-9985 (Electronic)
IS  - 1545-9993 (Print)
IS  - 1545-9985 (Linking)
VI  - 16
IP  - 12
DP  - 2009 Dec
TI  - Structural basis of ligand binding by a c-di-GMP riboswitch.
PG  - 1218-23
LID - 10.1038/nsmb.1702 [doi]
AB  - The second messenger signaling molecule bis-(3'-5')-cyclic dimeric guanosine 
      monophosphate (c-di-GMP) regulates many processes in bacteria, including 
      motility, pathogenesis and biofilm formation. c-di-GMP-binding riboswitches are 
      important downstream targets in this signaling pathway. Here we report the 
      crystal structure, at 2.7 A resolution, of a c-di-GMP riboswitch aptamer from 
      Vibrio cholerae bound to c-di-GMP, showing that the ligand binds within a 
      three-helix junction that involves base-pairing and extensive base-stacking. The 
      symmetric c-di-GMP is recognized asymmetrically with respect to both the bases 
      and the backbone. A mutant aptamer was engineered that preferentially binds the 
      candidate signaling molecule c-di-AMP over c-di-GMP. Kinetic and structural data 
      suggest that genetic regulation by the c-di-GMP riboswitch is kinetically 
      controlled and that gene expression is modulated through the stabilization of a 
      previously unidentified P1 helix, illustrating a direct mechanism for c-di-GMP 
      signaling.
FAU - Smith, Kathryn D
AU  - Smith KD
AD  - Department of Chemistry, Yale University, New Haven, Connecticut, USA.
FAU - Lipchock, Sarah V
AU  - Lipchock SV
FAU - Ames, Tyler D
AU  - Ames TD
FAU - Wang, Jimin
AU  - Wang J
FAU - Breaker, Ronald R
AU  - Breaker RR
FAU - Strobel, Scott A
AU  - Strobel SA
LA  - eng
GR  - GM02278/GM/NIGMS NIH HHS/United States
GR  - P30 EB009998/EB/NIBIB NIH HHS/United States
GR  - P01 GM022778/GM/NIGMS NIH HHS/United States
GR  - P01 GM022778-347368/GM/NIGMS NIH HHS/United States
GR  - P01 GM022778-310003/GM/NIGMS NIH HHS/United States
GR  - P01 GM022778-357368/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20091108
PL  - United States
TA  - Nat Struct Mol Biol
JT  - Nature structural & molecular biology
JID - 101186374
RN  - 0 (Dinucleoside Phosphates)
RN  - 0 (Intercalating Agents)
RN  - 0 (RNA, Bacterial)
RN  - 0 (cyclic diadenosine phosphate)
RN  - 61093-23-0 (bis(3',5')-cyclic diguanylic acid)
RN  - H2D2X058MU (Cyclic GMP)
SB  - IM
CIN - Nat Struct Mol Biol. 2009 Dec;16(12):1201. PMID: 19956202
MH  - Base Pairing
MH  - Crystallography, X-Ray
MH  - Cyclic GMP/*analogs & derivatives/chemistry/metabolism
MH  - Dinucleoside Phosphates/metabolism
MH  - *Gene Expression Regulation, Bacterial
MH  - Intercalating Agents
MH  - Kinetics
MH  - Models, Molecular
MH  - Nucleic Acid Conformation
MH  - RNA, Bacterial/*chemistry/genetics/*metabolism
MH  - Scattering, Small Angle
MH  - Second Messenger Systems/*physiology
MH  - Vibrio cholerae/chemistry/*physiology
PMC - PMC2850612
MID - NIHMS191190
EDAT- 2009/11/10 06:00
MHDA- 2009/12/31 06:00
PMCR- 2010/06/01
CRDT- 2009/11/10 06:00
PHST- 2009/07/13 00:00 [received]
PHST- 2009/09/15 00:00 [accepted]
PHST- 2009/11/10 06:00 [entrez]
PHST- 2009/11/10 06:00 [pubmed]
PHST- 2009/12/31 06:00 [medline]
PHST- 2010/06/01 00:00 [pmc-release]
AID - nsmb.1702 [pii]
AID - 10.1038/nsmb.1702 [doi]
PST - ppublish
SO  - Nat Struct Mol Biol. 2009 Dec;16(12):1218-23. doi: 10.1038/nsmb.1702. Epub 2009 
      Nov 8.