Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Structure
2009 Mar 11;173:472-81. doi: 10.1016/j.str.2008.12.022.
Show Gene links
Show Anatomy links
Structure and biological function of the RNA pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus.
Messing SA
,
Gabelli SB
,
Liu Q
,
Celesnik H
,
Belasco JG
,
Piñeiro SA
,
Amzel LM
.
???displayArticle.abstract???
Until recently, the mechanism of mRNA decay in bacteria was thought to be different from that of eukaryotes. This paradigm changed with the discovery that RppH (ORF176/NudH/YgdP), an Escherichia coli enzyme that belongs to the Nudix superfamily, is an RNA pyrophosphohydrolase that initiates mRNA decay by cleaving pyrophosphate from the 5'-triphosphate. Here we report the 1.9 Angstroms resolution structure of the Nudix hydrolase BdRppH from Bdellovibrio bacteriovorus, a bacterium that feeds on other Gram-negative bacteria. Based on the structure of the enzyme alone and in complex with GTP-Mg2+, we propose a mode of RNA binding similar to that of the nuclear decapping enzyme from Xenopus laevis, X29. In additional experiments, we show that BdRppH can indeed function in vitro and in vivo as an RNA pyrophosphohydrolase. These findings set the basis for the identification of possible decapping enzymes in other bacteria.
Acker,
Reconstitution of yeast translation initiation.
2007, Pubmed
Acker,
Reconstitution of yeast translation initiation.
2007,
Pubmed
Bail,
Tri- to be mono- for bacterial mRNA decay.
2009,
Pubmed
Bessman,
The gene ygdP, associated with the invasiveness of Escherichia coli K1, designates a Nudix hydrolase, Orf176, active on adenosine (5')-pentaphospho-(5')-adenosine (Ap5A).
2001,
Pubmed
Bouvet,
Control of RNase E-mediated RNA degradation by 5'-terminal base pairing in E. coli.
1992,
Pubmed
Callaghan,
Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover.
2005,
Pubmed
Celesnik,
Initiation of RNA decay in Escherichia coli by 5' pyrophosphate removal.
2007,
Pubmed
Collaborative Computational Project, Number 4,
The CCP4 suite: programs for protein crystallography.
1994,
Pubmed
Conyers,
Metal requirements of a diadenosine pyrophosphatase from Bartonella bacilliformis: magnetic resonance and kinetic studies of the role of Mn2+.
2000,
Pubmed
Deana,
The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal.
2008,
Pubmed
Deshmukh,
mRNA decapping is promoted by an RNA-binding channel in Dcp2.
2008,
Pubmed
Dudev,
Factors governing the substitution of La3+ for Ca2+ and Mg2+ in metalloproteins: a DFT/CDM study.
2005,
Pubmed
Emory,
A 5'-terminal stem-loop structure can stabilize mRNA in Escherichia coli.
1992,
Pubmed
Fletcher,
The structure of Ap(4)A hydrolase complexed with ATP-MgF(x) reveals the basis of substrate binding.
2002,
Pubmed
Frick,
Dual divalent cation requirement of the MutT dGTPase. Kinetic and magnetic resonance studies of the metal and substrate complexes.
1994,
Pubmed
Gabelli,
The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family.
2001,
Pubmed
Gabelli,
Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase.
2002,
Pubmed
Gabelli,
Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus.
2004,
Pubmed
Garneau,
The highways and byways of mRNA decay.
2007,
Pubmed
Glusker,
Structural aspects of metal liganding to functional groups in proteins.
1991,
Pubmed
Gouet,
ESPript: analysis of multiple sequence alignments in PostScript.
1999,
Pubmed
Harris,
Mutational, kinetic, and NMR studies of the roles of conserved glutamate residues and of lysine-39 in the mechanism of the MutT pyrophosphohydrolase.
2000,
Pubmed
Jones,
Electron-density map interpretation.
1997,
Pubmed
Jones,
Improved methods for building protein models in electron density maps and the location of errors in these models.
1991,
Pubmed
Kang,
Structure of a coenzyme A pyrophosphatase from Deinococcus radiodurans: a member of the Nudix family.
2003,
Pubmed
Kang,
Structure and mechanism of MT-ADPRase, a nudix hydrolase from Mycobacterium tuberculosis.
2003,
Pubmed
Laskowski,
Main-chain bond lengths and bond angles in protein structures.
1993,
Pubmed
Mackie,
Ribonuclease E is a 5'-end-dependent endonuclease.
1998,
Pubmed
Mildvan,
Structures and mechanisms of Nudix hydrolases.
2005,
Pubmed
Morris,
Stereochemical quality of protein structure coordinates.
1992,
Pubmed
Navaza,
Implementation of molecular replacement in AMoRe.
2001,
Pubmed
Otwinowski,
Processing of X-ray diffraction data collected in oscillation mode.
1997,
Pubmed
Piccirillo,
Functional characterization of the mammalian mRNA decapping enzyme hDcp2.
2003,
Pubmed
Rendulic,
A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective.
2004,
Pubmed
Scarsdale,
Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes.
2006,
Pubmed
,
Xenbase
Schoenberg,
The end defines the means in bacterial mRNA decay.
2007,
Pubmed
She,
Structural basis of dcp2 recognition and activation by dcp1.
2008,
Pubmed
Sockett,
Bdellovibrio as therapeutic agents: a predatory renaissance?
2004,
Pubmed
Steyert,
Identification of Bdellovibrio bacteriovorus HD100 Bd0714 as a Nudix dGTPase.
2008,
Pubmed
STOLP,
BDELLOVIBRIO BACTERIOVORUS GEN. ET SP. N., A PREDATORY, ECTOPARASITIC, AND BACTERIOLYTIC MICROORGANISM.
1963,
Pubmed
Strauch,
Predatory mechanisms of Bdellovibrio and like organisms.
2007,
Pubmed
Swarbrick,
The three-dimensional structure of the Nudix enzyme diadenosine tetraphosphate hydrolase from Lupinus angustifolius L.
2000,
Pubmed
Terwilliger,
Maximum-likelihood density modification.
2000,
Pubmed
Terwilliger,
Automated MAD and MIR structure solution.
1999,
Pubmed
Terwilliger,
SOLVE and RESOLVE: automated structure solution and density modification.
2003,
Pubmed
Tock,
The CafA protein required for the 5'-maturation of 16 S rRNA is a 5'-end-dependent ribonuclease that has context-dependent broad sequence specificity.
2000,
Pubmed
van Ham,
Reductive genome evolution in Buchnera aphidicola.
2003,
Pubmed
Wang,
The hDcp2 protein is a mammalian mRNA decapping enzyme.
2002,
Pubmed
Xu,
RNA degradation in Escherichia coli regulated by 3' adenylation and 5' phosphorylation.
1995,
Pubmed
