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PDBsum entry 1mm2
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DNA binding protein
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PDB id
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1mm2
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Contents |
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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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Engineering a protein scaffold from a phd finger.
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Authors
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A.H.Kwan,
D.A.Gell,
A.Verger,
M.Crossley,
J.M.Matthews,
J.P.Mackay.
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Ref.
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Structure, 2003,
11,
803-813.
[DOI no: ]
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PubMed id
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Abstract
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The design of proteins with tailored functions remains a relatively elusive
goal. Small size, a well-defined structure, and the ability to maintain
structural integrity despite multiple mutations are all desirable properties for
such designer proteins. Many zinc binding domains fit this description. We
determined the structure of a PHD finger from the transcriptional cofactor
Mi2beta and investigated the suitability of this domain as a scaffold for
presenting selected binding functions. The two flexible loops in the structure
were mutated extensively by either substitution or expansion, without affecting
the overall fold of the domain. A binding site for the corepressor CtBP2 was
also grafted onto the domain, creating a new PHD domain that can specifically
bind CtBP2 both in vitro and in the context of a eukaryotic cell nucleus. These
results represent a step toward designing new regulatory proteins for modulating
aberrant gene expression in vivo.
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Figure 2.
Figure 2. Solution Structures of Mi2b-P2 and Structure
Comparisons with PHDs from WSTF and KAP-1(A) Ensemble of the
best 20 structures of Mi2b-P2. Structures are superimposed over
the backbone atoms (C^a, C', N) of residues 9-43 and 48-53
(residues 1-7 and 55-61, which are unstructured, are omitted for
clarity). The zinc-chelating side chains are shown in yellow and
green, and the zinc atom is shown in magenta. The L1 and L3
loops are shown in blue and red, respectively.(B) Ribbon diagram
of the lowest energy structure of Mi2b-P2, showing elements of
secondary structure as recognized in the program MOLMOL (Koradi
et al., 1996). Structures in (A) and (B) are shown as wall-eyed
stereo images.(C and D) Overlay of ribbon diagrams of the lowest
energy structures of Mi2b-P2 and the solution structure of the
PHDs from (C) WSTF and (D) KAP-1. Structures are superimposed
over the backbone atoms (C^a, C', N) of residues 9-43 and 48-53
in Mi2b-P2 and the corresponding residues in WSTF-PHD and
KAP-1-PHD, respectively. End terminal unstructured residues are
omitted for clarity.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2003,
11,
803-813)
copyright 2003.
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