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PDBsum entry 3k70
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Hydrolase/DNA
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PDB id
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3k70
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Contents |
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1155 a.a.
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1121 a.a.
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547 a.a.
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References listed in PDB file
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Key reference
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Title
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Dna binding to recd: role of the 1b domain in sf1b helicase activity.
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Authors
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K.Saikrishnan,
S.P.Griffiths,
N.Cook,
R.Court,
D.B.Wigley.
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Ref.
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Embo J, 2008,
27,
2222-2229.
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PubMed id
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Abstract
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The molecular mechanism of superfamily 1Balpha helicases remains unclear. We
present here the crystal structure of the RecD2 helicase from Deinococcus
radiodurans at 2.2-A resolution. The structure reveals the folds of the 1B and
2B domains of RecD that were poorly ordered in the structure of the Escherichia
coli RecBCD enzyme complex reported previously. The 2B domain adopts an SH3 fold
which, although common in eukaryotes, is extremely rare in bacterial systems. In
addition, the D. radiodurans RecD2 structure has aided us in deciphering lower
resolution (3.6 A) electron density maps for the E. coli RecBCD enzyme in
complex with a long DNA substrate that interacts with the RecD subunit. Taken
together, these structures indicated an important role for the 1B domain of
RecD, a beta-hairpin that extends from the surface of the 1A domain and
interacts with the DNA substrate. On the basis of these structural data, we
designed a mutant RecD2 helicase that lacks this pin. The 'pin-less' mutant
protein is a fully active ssDNA-dependent ATPase but totally lacks helicase
activity.
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Secondary reference #1
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Title
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Crystal structure of recbcd enzyme reveals a machine for processing DNA breaks.
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Authors
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M.R.Singleton,
M.S.Dillingham,
M.Gaudier,
S.C.Kowalczykowski,
D.B.Wigley.
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Ref.
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Nature, 2004,
432,
187-193.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2: Structures of the individual RecBCD subunits. a,
Domain structure of the RecB subunit. b, Close-up of the active
site of the nuclease. The calcium ion (grey sphere) is
coordinated to the side chains of three residues (His 956, Asp
1067 and Asp 1080) and the main-chain carbonyl of Tyr 1081. c,
Domain structure of the RecC subunit. The pin region is
highlighted. d, Space-filling representation of RecC, showing
the channels through the protein in the same colour scheme as in
c. e, Close-up view of the pin region in RecC, showing how the
DNA duplex is split across this feature of the RecC protein. f,
Domain structure of the RecD subunit. Domains 2 and 3 are
equivalent to the canonical 1A and 2A domains of other SF1
helicases. The images in a, and also those in Figs 2 and 4, were
created with PyMOL (Email: http://www.pymol.org).
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Figure 4.
Figure 4: Alternative exits from the 3' tunnel. a, Cutaway
view of the exit channels running each side of the nuclease
domain. The calcium ion at the nuclease active site is coloured
yellow. For the purposes of this figure, the loop that blocks
the channel has been omitted. There are two exit channels from
the RecC subunit. One of these (labelled 1) bypasses the
nuclease site. Access to the nuclease active site through
channel 2 is blocked by a helix in the structure. b, The
interface between the RecC subunit and the RecB nuclease domain
viewed across the RecB nuclease active site. RecC is shown in
blue as a space-filling representation, with the region affected
in the RecC* mutants highlighted in magenta. The RecB nuclease
domain is overlaid as an orange ribbon and the bound calcium ion
as a yellow sphere. Access to the nuclease active site from the
channel is blocked by a loop from the nuclease domain that
includes an  -helix
(residues 909 -930, coloured green).
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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