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PDBsum entry 3fms
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Transcription regulator
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PDB id
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3fms
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References listed in PDB file
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Key reference
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Title
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Structure of thermotoga maritima tm0439: implications for the mechanism of bacterial gntr transcription regulators with zn2+-Binding fcd domains.
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Authors
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M.Zheng,
D.R.Cooper,
N.E.Grossoehme,
M.Yu,
L.W.Hung,
M.Cieslik,
U.Derewenda,
S.A.Lesley,
I.A.Wilson,
D.P.Giedroc,
Z.S.Derewenda.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2009,
65,
356-365.
[DOI no: ]
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PubMed id
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Note: In the PDB file this reference is
annotated as "TO BE PUBLISHED". The citation details given above have
been manually determined.
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Abstract
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The GntR superfamily of dimeric transcription factors, with more than 6200
members encoded in bacterial genomes, are characterized by N-terminal
winged-helix DNA-binding domains and diverse C-terminal regulatory domains which
provide a basis for the classification of the constituent families. The largest
of these families, FadR, contains nearly 3000 proteins with all-alpha-helical
regulatory domains classified into two related Pfam families: FadR_C and FCD.
Only two crystal structures of FadR-family members, those of Escherichia coli
FadR protein and LldR from Corynebacterium glutamicum, have been described to
date in the literature. Here, the crystal structure of TM0439, a GntR regulator
with an FCD domain found in the Thermotoga maritima genome, is described. The
FCD domain is similar to that of the LldR regulator and contains a buried
metal-binding site. Using atomic absorption spectroscopy and Trp fluorescence,
it is shown that the recombinant protein contains bound Ni(2+) ions but that it
is able to bind Zn(2+) with K(d) < 70 nM. It is concluded that Zn(2+) is the
likely physiological metal and that it may perform either structural or
regulatory roles or both. Finally, the TM0439 structure is compared with two
other FadR-family structures recently deposited by structural genomics
consortia. The results call for a revision in the classification of the FadR
family of transcription factors.
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Figure 4.
Figure 4 The dimerization interfaces of the FCD and FadR_C
domains. For TM0439, two complete FCD domains are shown, with
one monomer colored as in Fig. 3-. Residues described in the
text are represented as sticks. For the other structures only
the helices that participate in dimerization are shown.
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Figure 5.
Figure 5 Metal-binding sites of TM0439 (PDB code 3fms ),
CGL2915 (2di3 ) and PS5454 (3c7j ). An OMIT map contoured at 5
 is
shown for TM0439. This was generated by deleting the metal and
acetate and truncating the histidines back to the C^  atoms,
shaking the coordinates to yield an r.m.s.d. of 0.3 Å and
performing a round of refinement in phexix.refine.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2009,
65,
356-365)
copyright 2009.
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