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PDBsum entry 2cvh
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DNA binding protein
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PDB id
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2cvh
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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 radb recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis kod1: an implication for the formation of a near-7-Fold helical assembly.
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Authors
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T.Akiba,
N.Ishii,
N.Rashid,
M.Morikawa,
T.Imanaka,
K.Harata.
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Ref.
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Nucleic Acids Res, 2005,
33,
3412-3423.
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PubMed id
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Abstract
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The X-ray crystal structure of RadB from Thermococcus kodakaraensis KOD1, an
archaeal homologue of the RecA/Rad51 family proteins, have been determined in
two crystal forms. The structure represents the core ATPase domain of the
RecA/Rad51 proteins. Two independent molecules in the type 1 crystal were
roughly related by 7-fold screw symmetry whereas non-crystallographic 2-fold
symmetry was observed in the type 2 crystal. The dimer structure in the type 1
crystal is extended to construct a helical assembly, which resembles the
filamentous structures reported for other RecA/Rad51 proteins. The molecular
interface in the type 1 dimer is formed by facing a basic surface patch of one
monomer to an acidic one of the other. The empty ATP binding pocket is located
at the interface and barely concealed from the outside similarly to that in the
active form of the RecA filament. The model assembly has a positively charged
belt on one surface bordering the helical groove suitable for facile binding of
DNA. Electron microscopy has revealed that, in the absence of ATP and DNA, RadB
forms a filament with a similar diameter to that of the hypothetical assembly,
although its helical properties were not confirmed.
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Figure 1.
Ribbon representation of TkRadB.
denoted by H1-H7 and S1-S9, respectively, and the N- and C-terminals by N and C,
respectively. The L1 and L2 loops are also labelled. Side-chains of Lys-33, Thr-34 and
Asp-112 are presented as ball-and-stick models to show the location of the ATP binding
site; the first two of the Walker A motif are in green and the last one of the Walker B
motif in cyan.
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Figure 3.
Structures of the asymmetric unit of the type 1 crystal (a) and the type 2
crystal (b). Side-chains of Lys-33, Thr-34 and Asp-112 in each monomer are presented as
ball-and-stick models as in Figure 1. In (b), the non-crystallographic 2-fold
rotation axis is perpendicular to the figure plane.
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The above figures are
reprinted
from an Open Access publication published by Oxford University Press:
Nucleic Acids Res
(2005,
33,
3412-3423)
copyright 2005.
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