PDBsum entry 2a6r

Toxin

PDB id

2a6r

Loading ...

Contents

			Protein chains

					(+ 0 more) 84 a.a. *

			Metals

					_MG ×2

			Waters ×352

* Residue conservation analysis

PDB id:

2a6r

Links

Name:

Toxin

Title:

Crystal structure of yoeb under peg condition

Structure:

Toxin yoeb. Chain: a, b, c, d, e, f. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: yoeb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.05Å

R-factor:

0.196

R-free:

0.229

Authors:

K.Kamada,F.Hanaoka

Key ref:

K.Kamada and F.Hanaoka (2005). Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin. Mol Cell, 19, 497-509. PubMed id: 16109374 DOI: 10.1016/j.molcel.2005.07.004

Date:

04-Jul-05

Release date:

23-Aug-05

PROCHECK

	Headers

	References

Protein chains

P69348 (YOEB_ECOLI) - Toxin YoeB from Escherichia coli (strain K12)

Seq: Struc:					84 a.a. 84 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.1.-.-

[IntEnz] [ExPASy] [KEGG] [BRENDA]

DOI no: 10.1016/j.molcel.2005.07.004	Mol Cell 19:497-509 (2005)
PubMed id: 16109374

Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin.
K.Kamada, F.Hanaoka.

ABSTRACT

The eubacterial chromosome encodes various addiction modules that control global levels of translation through RNA degradation. Crystal structures of the Escherichia coli YefM2 (antitoxin)-YoeB (toxin) complex and the free YoeB toxin have been determined. The structure of the heterotrimeric complex reveals an asymmetric disorder-to-order recognition strategy, in which one C terminus of the YefM homodimer exclusively interacts with an atypical microbial ribonuclease (RNase) fold of YoeB. Comparison with the YefM-free YoeB structure indicates a conformational rearrangement of the RNase catalytic site of YoeB, induced by interaction with YefM. Complementary biochemical experiments demonstrate that the YoeB toxin has an in vitro RNase activity that preferentially cleaves at the 3' end of purine ribonucleotides.

Selected figure(s)



	Figure 2. Figure 2. Structure of the YefM-YoeB Heterotrimer Complex		Figure 5. Figure 5. Protein-Protein Interactions between YefM and YoeB

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21030436

E.M.Halvorsen, J.J.Williams, A.J.Bhimani, E.A.Billings, and P.J.Hergenrother (2011).
Txe, an endoribonuclease of the enterococcal Axe-Txe toxin-antitoxin system, cleaves mRNA and inhibits protein synthesis.

Microbiology, 157, 387-397.

21166897

Q.Tan, N.Awano, and M.Inouye (2011).
YeeV is an Escherichia coli toxin that inhibits cell division by targeting the cytoskeleton proteins, FtsZ and MreB.

Mol Microbiol, 79, 109-118.

21315267

T.R.Blower, G.P.Salmond, and B.F.Luisi (2011).
Balancing at survival's edge: the structure and adaptive benefits of prokaryotic toxin-antitoxin partners.

Curr Opin Struct Biol, 21, 109-118.

21323758

Y.Zhang, and M.Inouye (2011).
RatA (YfjG), an Escherichia coli toxin, inhibits 70S ribosome association to block translation initiation.

Mol Microbiol, 79, 1418-1429.

20677831

C.Göbl, S.Kosol, T.Stockner, H.M.Rückert, and K.Zangger (2010).
Solution structure and membrane binding of the toxin fst of the par addiction module.

Biochemistry, 49, 6567-6575.

PDB code:

2kv5

20585658

C.Nieto, E.Sadowy, A.G.de la Campa, W.Hryniewicz, and M.Espinosa (2010).
The relBE2Spn toxin-antitoxin system of Streptococcus pneumoniae: role in antibiotic tolerance and functional conservation in clinical isolates.

PLoS One, 5, e11289.

20143871

K.M.Dalton, and S.Crosson (2010).
A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex.

Biochemistry, 49, 2205-2215.

PDB code:

3kxe

20975905

L.C.Barbosa, S.S.Garrido, A.Garcia, D.B.Delfino, and R.Marchetto (2010).
Function inferences from a molecular structural model of bacterial ParE toxin.

Bioinformation, 4, 438-440.

20696400

M.A.Arbing, S.K.Handelman, A.P.Kuzin, G.Verdon, C.Wang, M.Su, F.P.Rothenbacher, M.Abashidze, M.Liu, J.M.Hurley, R.Xiao, T.Acton, M.Inouye, G.T.Montelione, N.A.Woychik, and J.F.Hunt (2010).
Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems.

Structure, 18, 996.

PDB codes:

2h28 2ict 2inw 3kh2

19943910

M.Christensen-Dalsgaard, M.G.Jørgensen, and K.Gerdes (2010).
Three new RelE-homologous mRNA interferases of Escherichia coli differentially induced by environmental stresses.

Mol Microbiol, 75, 333-348.

21129205

M.Uzan, and E.S.Miller (2010).
Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation.

Virol J, 7, 360.

20022964

S.Agarwal, N.K.Mishra, S.Bhatnagar, and R.Bhatnagar (2010).
PemK toxin of Bacillus anthracis is a ribonuclease: an insight into its active site, structure, and function.

J Biol Chem, 285, 7254-7270.

20041169

B.L.Brown, S.Grigoriu, Y.Kim, J.M.Arruda, A.Davenport, T.K.Wood, W.Peti, and R.Page (2009).
Three dimensional structure of the MqsR:MqsA complex: a novel TA pair comprised of a toxin homologous to RelE and an antitoxin with unique properties.

PLoS Pathog, 5, e1000706.

PDB codes:

3fmy 3ga8 3gn5 3hi2

20005802

C.Neubauer, Y.G.Gao, K.R.Andersen, C.M.Dunham, A.C.Kelley, J.Hentschel, K.Gerdes, V.Ramakrishnan, and D.E.Brodersen (2009).
The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE.

Cell, 139, 1084-1095.

PDB codes:

3kha 3kiq 3kir 3kis 3kit 3kiu 3kiw 3kix 3kiy

19143615

C.R.Cooper, A.J.Daugherty, S.Tachdjian, P.H.Blum, and R.M.Kelly (2009).
Role of vapBC toxin-antitoxin loci in the thermal stress response of Sulfolobus solfataricus.

Biochem Soc Trans, 37, 123-126.

19297318

G.Y.Li, Y.Zhang, M.Inouye, and M.Ikura (2009).
Inhibitory Mechanism of Escherichia coli RelE-RelB Toxin-Antitoxin Module Involves a Helix Displacement Near an mRNA Interferase Active Site.

J Biol Chem, 284, 14628-14636.

PDB codes:

2kc8 2kc9

19423702

J.M.Hurley, and N.A.Woychik (2009).
Bacterial Toxin HigB Associates with Ribosomes and Mediates Translation-dependent mRNA Cleavage at A-rich Sites.

J Biol Chem, 284, 18605-18613.

19251861

L.Zhu, K.Inoue, S.Yoshizumi, H.Kobayashi, Y.Zhang, M.Ouyang, F.Kato, M.Sugai, and M.Inouye (2009).
Staphylococcus aureus MazF specifically cleaves a pentad sequence, UACAU, which is unusually abundant in the mRNA for pathogenic adhesive factor SraP.

J Bacteriol, 191, 3248-3255.

19060138

M.G.Jørgensen, D.P.Pandey, M.Jaskolska, and K.Gerdes (2009).
HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea.

J Bacteriol, 191, 1191-1199.

19747491

M.Overgaard, J.Borch, and K.Gerdes (2009).
RelB and RelE of Escherichia coli form a tight complex that represses transcription via the ribbon-helix-helix motif in RelB.

J Mol Biol, 394, 183-196.

19028895

S.E.Bailey, and F.Hayes (2009).
Influence of operator site geometry on transcriptional control by the YefM-YoeB toxin-antitoxin complex.

J Bacteriol, 191, 762-772.

19581360

S.Yoshizumi, Y.Zhang, Y.Yamaguchi, L.Chen, B.N.Kreiswirth, and M.Inouye (2009).
Staphylococcus aureus YoeB homologues inhibit translation initiation.

J Bacteriol, 191, 5868-5872.

19690171

Y.Yamaguchi, J.H.Park, and M.Inouye (2009).
MqsR, a crucial regulator for quorum sensing and biofilm formation, is a GCU-specific mRNA interferase in Escherichia coli.

J Biol Chem, 284, 28746-28753.

19124462

Y.Zhang, and M.Inouye (2009).
The Inhibitory Mechanism of Protein Synthesis by YoeB, an Escherichia coli Toxin.

J Biol Chem, 284, 6627-6638.

19617347

Y.Zhang, Y.Yamaguchi, and M.Inouye (2009).
Characterization of YafO, an Escherichia coli toxin.

J Biol Chem, 284, 25522-25531.

18757857

A.Garcia-Pino, M.Christensen-Dalsgaard, L.Wyns, M.Yarmolinsky, R.D.Magnuson, K.Gerdes, and R.Loris (2008).
Doc of Prophage P1 Is Inhibited by Its Antitoxin Partner Phd through Fold Complementation.

J Biol Chem, 283, 30821-30827.

PDB code:

3dd7

18997335

A.Garcia-Pino, M.H.Dao-Thi, E.Gazit, R.D.Magnuson, L.Wyns, and R.Loris (2008).
Crystallization of Doc and the Phd-Doc toxin-antitoxin complex.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1034-1038.

18377929

F.Garza-Sánchez, J.G.Gin, and C.S.Hayes (2008).
Amino acid starvation and colicin D treatment induce A-site mRNA cleavage in Escherichia coli.

J Mol Biol, 378, 505-519.

17957768

K.D.Han, S.J.Park, S.B.Jang, and B.J.Lee (2008).
Solution structure of conserved hypothetical protein HP0892 from Helicobacter pylori.

Proteins, 70, 599-602.

PDB code:

2otr

18854355

M.Christensen-Dalsgaard, and K.Gerdes (2008).
Translation affects YoeB and MazF messenger RNA interferase activities by different mechanisms.

Nucleic Acids Res, 36, 6472-6481.

18532983

M.Overgaard, J.Borch, M.G.Jørgensen, and K.Gerdes (2008).
Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity.

Mol Microbiol, 69, 841-857.

17170003

B.Kedzierska, L.Y.Lian, and F.Hayes (2007).
Toxin-antitoxin regulation: bimodal interaction of YefM-YoeB with paired DNA palindromes exerts transcriptional autorepression.

Nucleic Acids Res, 35, 325-339.

17046813

B.Odaert, F.Saïda, P.Aliprandi, S.Durand, J.B.Créchet, R.Guerois, S.Laalami, M.Uzan, and F.Bontems (2007).
Structural and functional studies of RegB, a new member of a family of sequence-specific ribonucleases involved in mRNA inactivation on the ribosome.

J Biol Chem, 282, 2019-2028.

PDB code:

2hx6

17560162

C.Condon (2007).
Maturation and degradation of RNA in bacteria.

Curr Opin Microbiol, 10, 271-278.

17071753

C.Nieto, I.Cherny, S.K.Khoo, M.G.de Lacoba, W.T.Chan, C.C.Yeo, E.Gazit, and M.Espinosa (2007).
The yefM-yoeB toxin-antitoxin systems of Escherichia coli and Streptococcus pneumoniae: functional and structural correlation.

J Bacteriol, 189, 1266-1278.

17317682

M.C.Monti, A.M.Hernández-Arriaga, M.B.Kamphuis, J.López-Villarejo, A.J.Heck, R.Boelens, R.Díaz-Orejas, and R.H.van den Heuvel (2007).
Interactions of Kid-Kis toxin-antitoxin complexes with the parD operator-promoter region of plasmid R1 are piloted by the Kis antitoxin and tuned by the stoichiometry of Kid-Kis oligomers.

Nucleic Acids Res, 35, 1737-1749.

17656583

M.Oberer, K.Zangger, K.Gruber, and W.Keller (2007).
The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding.

Protein Sci, 16, 1676-1688.

PDB code:

2an7

17706670

O.Schmidt, V.J.Schuenemann, N.J.Hand, T.J.Silhavy, J.Martin, A.N.Lupas, and S.Djuranovic (2007).
prlF and yhaV encode a new toxin-antitoxin system in Escherichia coli.

J Mol Biol, 372, 894-905.

17263853

R.Motiejūnaite, J.Armalyte, A.Markuckas, and E.Suziedeliene (2007).
Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module.

FEMS Microbiol Lett, 268, 112-119.

17488720

S.K.Khoo, B.Loll, W.T.Chan, R.L.Shoeman, L.Ngoo, C.C.Yeo, and A.Meinhart (2007).
Molecular and structural characterization of the PezAT chromosomal toxin-antitoxin system of the human pathogen Streptococcus pneumoniae.

J Biol Chem, 282, 19606-19618.

PDB code:

2p5t

17513477

V.Tsilibaris, G.Maenhaut-Michel, N.Mine, and L.Van Melderen (2007).
What is the benefit to Escherichia coli of having multiple toxin-antitoxin systems in its genome?

J Bacteriol, 189, 6101-6108.

16803593

C.Condon (2006).
Shutdown decay of mRNA.

Mol Microbiol, 61, 573-583.

16982615

K.Mattison, J.S.Wilbur, M.So, and R.G.Brennan (2006).
Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs.

J Biol Chem, 281, 37942-37951.

PDB codes:

2bsq 2h1c 2h1o

17020579

M.Christensen-Dalsgaard, and K.Gerdes (2006).
Two higBA loci in the Vibrio cholerae superintegron encode mRNA cleaving enzymes and can stabilize plasmids.

Mol Microbiol, 62, 397-411.

17001682

M.Inouye (2006).
The discovery of mRNA interferases: implication in bacterial physiology and application to biotechnology.

J Cell Physiol, 209, 670-676.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.