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PDBsum entry 2dq5
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References listed in PDB file
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Key reference
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Title
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Solution structure of the mid1 b-Box2 chc(d/c)c(2)h(2) zinc-Binding domain: insights into an evolutionarily conserved ring fold.
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Authors
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M.A.Massiah,
J.A.Matts,
K.M.Short,
B.N.Simmons,
S.Singireddy,
Z.Yi,
T.C.Cox.
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Ref.
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J Mol Biol, 2007,
369,
1.
[DOI no: ]
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PubMed id
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Abstract
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The B-box type 2 domain is a prominent feature of a large and growing family of
RING, B-box, coiled-coil (RBCC) domain-containing proteins and is also present
in more than 1500 additional proteins. Most proteins usually contain a single
B-box2 domain, although some proteins contain tandem domains consisting of both
type 1 and type 2 B-boxes, which actually share little sequence similarity.
Recently, we determined the solution structure of B-box1 from MID1, a putative
E3 ubiquitin ligase that is mutated in X-linked Opitz G/BBB syndrome, and showed
that it adopted a betabetaalpha RING-like fold. Here, we report the tertiary
structure of the B-box2 (CHC(D/C)C(2)H(2)) domain from MID1 using
multidimensional NMR spectroscopy. This MID1 B-box2 domain consists of a short
alpha-helix and a structured loop with two short anti-parallel beta-strands and
adopts a tertiary structure similar to the B-box1 and RING structures, even
though there is minimal primary sequence similarity between these domains. By
mutagenesis, ESI-FTICR and ICP mass spectrometry, we show that the B-box2 domain
coordinates two zinc atoms with a 'cross-brace' pattern: one by Cys175, His178,
Cys195 and Cys198 and the other by Cys187, Asp190, His204, and His207.
Interestingly, this is the first case that an aspartic acid is involved in zinc
atom coordination in a zinc-finger domain, although aspartic acid has been shown
to coordinate non-catalytic zinc in matrix metalloproteinases. In addition, the
finding of a Cys195Phe substitution identified in a patient with X-linked Opitz
GBBB syndrome supports the importance of proper zinc coordination for the
function of the MID1 B-box2 domain. Notably, however, our structure differs from
the only other published B-box2 structure, that from XNF7, which was shown to
coordinate one zinc atom. Finally, the similarity in tertiary structures of the
B-box2, B-box1 and RING domains suggests these domains have evolved from a
common ancestor.
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Figure 2.
Figure 2. A surface representation of the B-box2 domain. (a)
The surface of the MID1 B-box2 domain showing basic patches
(colored blue) comprised of lysine and arginine residues, acidic
patches (colored red) of glutamic and aspartic acid residues,
and hydrophobic patches (colored green) formed by leucine,
isoleucine, alanine, tyrosine, methionine, and valine. All other
residues are white. Two spheres representing the two zinc atoms
and a ribbon drawing of B-box2 are depicted. Note the extensive
hydrophobic surface on the outer surface of the helix and
structured loop with the β-strands. This pattern of hydrophobic
surfaces and distinct charge patches is similar in the other
B-box2 domains, except TRIM29. (b) Hydrophobic and charge
distribution of TRIM29 B-box2, shown in the same orientation as
MID1 B-box2 in (a) (left). The other side of TRIM29 B-box2 (not
shown) is predominately hydrophobic. Notably, the surface above
the structured loop with the two β-strands is hydrophobic,
similar to MID1 B-box2; however, a C-terminal helix packs
against this surface, suggesting a possible domain–domain
interface. (c) The superposition of MID1 B-box1 (green) and
B-box2 (red) showing the overall similarity in secondary and
tertiary structures, even though their primary sequences are not
homologous. The relative locations of the zinc ions (shown as
green and red balls) are also similar.
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Figure 3.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
369,
1-0)
copyright 2007.
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