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PDBsum entry 1x3f
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DNA binding protein
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PDB id
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1x3f
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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 mycobacterium smegmatis single-Stranded DNA-Binding protein and a comparative study involving homologus ssbs: biological implications of structural plasticity and variability in quaternary association.
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Authors
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K.Saikrishnan,
G.P.Manjunath,
P.Singh,
J.Jeyakanthan,
Z.Dauter,
K.Sekar,
K.Muniyappa,
M.Vijayan.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2005,
61,
1140-1148.
[DOI no: ]
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PubMed id
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Abstract
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The structure of Mycobacterium smegmatis single-stranded DNA-binding protein
(SSB) has been determined using three data sets collected from related crystals.
The structure is similar to that of its homologue from Mycobacterium
tuberculosis, indicating that the clamp arrangement that stabilizes the dimer
and the ellipsoidal shape of the tetramer are characteristic features of
mycobacterial SSBs. The central OB fold is conserved in mycobacterial SSBs as
well as those from Escherichia coli, Deinococcus radiodurans and human
mitochondria. However, the quaternary structure exhibits considerable
variability. The observed plasticity of the subunit is related to this
variability. The crystal structures and modelling provide a rationale for the
variability. The strand involved in the clamp mechanism, which leads to higher
stability of the tetramer, appears to occur in all high-G+C Gram-positive
bacteria. The higher stability is perhaps required by these organisms. The mode
of DNA binding of mycobacterial SSBs is different from that of E. coli SSB
partly on account of the difference in the shape of the tetramers. Another
difference between the two modes is that the former contains additional ionic
interactions and is more susceptible to salt concentration.
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Figure 1.
Figure 1
A 2F[o] - F[c] omit map for the stretch of residues 102-120. The figure was generated
using BOBSCRIPT (Esnouf, 1997 [Esnouf, R. M. (1997). J. Mol. Graph. 15,
132-134.]-[bluearr.gif] ). The map was contoured at 1 [sigma] .
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Figure 6.
Figure 6
Surface diagram of MsSSB, DrSSB and EcSSB viewed down the twofold axis P (represented as a
blue ball), highlighting the variation in the orientation of the OB folds. Subunits A and
C of MsSSB and EcSSB and subunit A of DrSSB were superposed onto one another (represented
in grey) to bring out the difference in the orientation of subunits B and D of MsSSB
(magenta) and EcSSB (red) and subunit B of DrSSB (green). The loops are omitted for
clarity.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2005,
61,
1140-1148)
copyright 2005.
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Secondary reference #1
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Title
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Structure of mycobacterium tuberculosis single-Stranded DNA-Binding protein. Variability in quaternary structure and its implications.
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Authors
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K.Saikrishnan,
J.Jeyakanthan,
J.Venkatesh,
N.Acharya,
K.Sekar,
U.Varshney,
M.Vijayan.
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Ref.
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J Mol Biol, 2003,
331,
385-393.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4. (a) Surface diagram of the MtuSSB dimer
illustrating the clamp-mechanism involving strand 9. (b)
Space-filling diagram of MtuSSB and EcoSSB tetramers with the
three loops removed, viewed down axis P. Subunits BD are
oriented identically in the two structures.
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Figure 5.
Figure 5. Spatial disposition of the three-stranded back
b-sheet in the tetramer and across the three interfaces in
different tetrameric SSBs. Subunit A is coloured magenta, B in
cyan, C in green and D in yellow. The gap between the two sheets
from subunits A and C (B and D) are bridged by water molecules
(blue) in Mtussb form I.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Crystallization and preliminary X-Ray studies of the single-Stranded DNA-Binding protein from mycobacterium tuberculosis.
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Authors
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K.Saikrishnan,
J.Jeyakanthan,
J.Venkatesh,
N.Acharya,
K.Purnapatre,
K.Sekar,
U.Varshney,
M.Vijayan.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2002,
58,
327-329.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 Crystals of MtSSB. (a) Form I, (b) form II.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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