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PDBsum entry 1jr3
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Contents |
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366 a.a.
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338 a.a.
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334 a.a.
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the processivity clamp loader gamma (gamma) complex of e. Coli DNA polymerase III.
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Authors
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D.Jeruzalmi,
M.O'Donnell,
J.Kuriyan.
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Ref.
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Cell, 2001,
106,
429-441.
[DOI no: ]
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PubMed id
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Abstract
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The gamma complex, an AAA+ ATPase, is the bacterial homolog of eukaryotic
replication factor C (RFC) that loads the sliding clamp (beta, homologous to
PCNA) onto DNA. The 2.7/3.0 A crystal structure of gamma complex reveals a
pentameric arrangement of subunits, with stoichiometry delta':gamma(3):delta.
The C-terminal domains of the subunits form a circular collar that supports an
asymmetric arrangement of the N-terminal ATP binding domains of the gamma motor
and the structurally related domains of the delta' stator and the delta wrench.
The structure suggests a mechanism by which the gamma complex switches between a
closed state, in which the beta-interacting element of delta is hidden by
delta', and an open form similar to the crystal structure, in which delta is
free to bind to beta.
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Figure 3.
Figure 3. γ:γ Interfacial Nucleotide Binding Sites
Compared to the NSF Homolog p97(A) The nucleotide binding site
of p97 (left) (Zhang et al., 2000) (PDB code 1E32) is compared
to that of γ2 (at the γ1-γ2 interface, middle) and of γ3 (at
the γ2-γ3 interface, right). For the γ structures, Domains I
and II are colored, and Domain III is shown in gray. A schematic
representation of the Domain I–II units is shown below the
structures. ADP bound to p97 is shown at the active site of γ2
(middle) and γ3 (right) for reference. The arginine side chains
of the Sensor 1 region are shown in dark blue at each
interface.(B) The Sensor 1 region of γ1 is buried at the
γ1-γ2 interface. On the left, the γ1-γ2 pair of subunits is
shown, with the molecular surface of γ2 colored in gray,
highlighted in red where γ1 contacts the γ2 surface. γ1 is
shown as a green tube representing the backbone, with the Sensor
1 region colored magenta. γ2 is shown with the surface removed
on the right
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Figure 4.
Figure 4. The δ′ Stator Is Unlikely to Cause Closure of
the Adjacent γ1 ATP Binding SiteOn the left, the γ1 (green)
and γ2 (red) pair of subunits is shown, with Sensor 1 of γ1
(magenta) positioned near the ATP binding site of γ2 (indicated
in gray). The first helix of Domain III of γ1, α10, is shown
as a magenta tube to highlight the flexible linker connecting it
to the last helix of Domain II. On the right, γ2 is shown
again, in the same orientation as on the left (red). The γ1
subunit is replaced by δ′ (orange), which has been
superimposed on γ1 using the C-terminal domain. Note that helix
α10 in δ′ is extended at its N terminus relative to the
structure seen in γ1, so that the connection to Domain II no
longer appears to be flexible. The overall conformation of δ′
is more closed than that of γ1, so that the Sensor 1 region of
δ′ is no longer located as close to the ATP binding site of
γ2 as that of γ1
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2001,
106,
429-441)
copyright 2001.
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