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* Residue conservation analysis
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Enzyme class 2:
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Chain A:
E.C.3.1.-.-
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Enzyme class 3:
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Chain B:
E.C.?
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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DOI no:
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J Biol Chem
281:37942-37951
(2006)
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PubMed id:
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Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs.
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K.Mattison,
J.S.Wilbur,
M.So,
R.G.Brennan.
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ABSTRACT
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Neisseria gonorrhoeae is a sexually transmitted pathogen that initiates
infections in humans by adhering to the mucosal epithelium of the urogenital
tract. The bacterium then enters the apical region of the cell and traffics
across the cell to exit into the subepithelial matrix. Mutations in the fast
intracellular trafficking (fitAB) locus cause the bacteria to transit a
polarized epithelial monolayer more quickly than the wild-type parent and to
replicate within cells at an accelerated rate. Here, we describe the crystal
structure of the toxin-antitoxin heterodimer, FitAB, bound to a high affinity
36-bp DNA fragment from the fitAB promoter. FitA, the antitoxin, binds DNA
through its ribbon-helix-helix motif and is tethered to FitB, the toxin, to form
a heterodimer by the insertion of a four turn alpha-helix into an extensive FitB
hydrophobic pocket. FitB is composed of a PIN (PilT N terminus) domain, with a
central, twisted, 5-stranded parallel beta-sheet that is open on one side and
flanked by five alpha-helices. FitB in the context of the FitAB complex does not
display nuclease activity against tested PIN substrates. The FitAB complex
points to the mechanism by which antitoxins with RHH motifs can block the
activity of toxins with PIN domains. Interactions between two FitB molecules
result in the formation of a tetramer of FitAB heterodimers, which binds to the
36-bp DNA fragment and provides an explanation for how FitB enhances the DNA
binding affinity of FitA.
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Selected figure(s)
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Figure 2.
FIGURE 2. Ribbon diagram of the structure of the FitAB-IR36
complex. a, the FitA and FitB proteins are colored magenta and
cyan, respectively. DNA is colored according to gray (carbon),
red (oxygen), blue (nitrogen), and yellow (phosphorus). The four
FitAB heterodimers are numbered from I to IV. b, view of a
rotated to demonstrate that the two FitA  sheets bind on the same
face of the DNA helix. c, sequence of the 36-bp IR36 site used
for crystallization. The 8-bp inverted repeat half-sites are
highlighted in yellow.
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Figure 4.
FIGURE 4. FitA-DNA contacts. a, schematic diagram of the
FitA-DNA contacts. The deoxyriboses of each nucleotide are
numbered, labeled, and shown as pentagons. Side chain DNA
hydrogen bonds are indicated by blue arrows, backbone amide-DNA
hydrogen bonds are green arrows, and van der Waals contacts are
shown as yellow arrows. Each FitA residue is from subunit I, II,
III, or IV, as defined in the legend to Fig. 2. b, stereo view
of the composite omit electron density map of one FitA-DNA
interface contoured at 1.0  to 3.0 Å
resolution (green mesh). The FitA protein is shown as magenta
balls and sticks and the DNA is shown as balls and sticks where
gray (carbon), red (oxygen), blue (nitrogen), yellow
(phosphorus). Note the water (Wat1)-mediated contact between
Asn^8 and Thy^32'.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
37942-37951)
copyright 2006.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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K.S.Winther,
and
K.Gerdes
(2011).
Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA.
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Proc Natl Acad Sci U S A,
108,
7403-7407.
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L.Huang,
P.Yin,
X.Zhu,
Y.Zhang,
and
K.Ye
(2011).
Crystal structure and centromere binding of the plasmid segregation protein ParB from pCXC100.
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Nucleic Acids Res,
39,
2954-2968.
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PDB code:
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N.Chopra,
S.Agarwal,
S.Verma,
S.Bhatnagar,
and
R.Bhatnagar
(2011).
Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function.
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J Comput Aided Mol Des,
25,
275-291.
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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.
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Curr Opin Struct Biol,
21,
109-118.
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V.L.Arcus,
J.L.McKenzie,
J.Robson,
and
G.M.Cook
(2011).
The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array.
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Protein Eng Des Sel,
24,
33-40.
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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.
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Biochemistry,
49,
6567-6575.
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PDB code:
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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.
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PLoS One,
5,
e11289.
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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.
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Structure,
18,
996.
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PDB codes:
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A.C.Lamanna,
and
K.Karbstein
(2009).
Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain.
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Proc Natl Acad Sci U S A,
106,
14259-14264.
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C.S.Hayes,
and
D.A.Low
(2009).
Signals of growth regulation in bacteria.
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Curr Opin Microbiol,
12,
667-673.
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F.Guillière,
N.Peixeiro,
A.Kessler,
B.Raynal,
N.Desnoues,
J.Keller,
M.Delepierre,
D.Prangishvili,
G.Sezonov,
and
J.I.Guijarro
(2009).
Structure, function, and targets of the transcriptional regulator SvtR from the hyperthermophilic archaeal virus SIRV1.
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J Biol Chem,
284,
22222-22237.
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PDB code:
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K.S.Winther,
and
K.Gerdes
(2009).
Ectopic production of VapCs from Enterobacteria inhibits translation and trans-activates YoeB mRNA interferase.
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Mol Microbiol,
72,
918-930.
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L.Miallau,
M.Faller,
J.Chiang,
M.Arbing,
F.Guo,
D.Cascio,
and
D.Eisenberg
(2009).
Structure and proposed activity of a member of the VapBC family of toxin-antitoxin systems. VapBC-5 from Mycobacterium tuberculosis.
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J Biol Chem,
284,
276-283.
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PDB code:
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L.Ni,
S.O.Jensen,
N.Ky Tonthat,
T.Berg,
S.M.Kwong,
F.H.Guan,
M.H.Brown,
R.A.Skurray,
N.Firth,
and
M.A.Schumacher
(2009).
The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes.
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Nucleic Acids Res,
37,
6970-6983.
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PDB code:
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M.Zampini,
A.Derome,
S.E.Bailey,
D.Barillà,
and
F.Hayes
(2009).
Recruitment of the ParG segregation protein to different affinity DNA sites.
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J Bacteriol,
191,
3832-3841.
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S.E.Bailey,
and
F.Hayes
(2009).
Influence of operator site geometry on transcriptional control by the YefM-YoeB toxin-antitoxin complex.
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J Bacteriol,
191,
762-772.
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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.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
1034-1038.
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R.D.Bunker,
J.L.McKenzie,
E.N.Baker,
and
V.L.Arcus
(2008).
Crystal structure of PAE0151 from Pyrobaculum aerophilum, a PIN-domain (VapC) protein from a toxin-antitoxin operon.
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Proteins,
72,
510-518.
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PDB code:
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Y.Zhou,
J.D.Larson,
C.A.Bottoms,
E.C.Arturo,
M.T.Henzl,
J.L.Jenkins,
J.C.Nix,
D.F.Becker,
and
J.J.Tanner
(2008).
Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA.
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J Mol Biol,
381,
174-188.
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PDB code:
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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.
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J Bacteriol,
189,
1266-1278.
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E.R.Schreiter,
and
C.L.Drennan
(2007).
Ribbon-helix-helix transcription factors: variations on a theme.
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Nat Rev Microbiol,
5,
710-720.
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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.
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Protein Sci,
16,
1676-1688.
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PDB code:
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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.
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Links
