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PDBsum entry 1njq
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Metal binding protein
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PDB id
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1njq
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Contents |
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* Residue conservation analysis
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PDB id:
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Metal binding protein
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Title:
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Nmr structure of the single qalggh zinc finger domain from arabidopsis thaliana superman protein
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Structure:
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Superman protein. Chain: a. Fragment: superman single qalggh zinc-finger domain. Engineered: yes
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Source:
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Synthetic: yes. Other_details: the peptide was chemically synthesized through fmoc solid state peptide synthesis. The sequence of the peptide is naturally found in arabidopsis thaliana.
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NMR struc:
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20 models
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Authors:
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C.Isernia,E.Bucci,M.Leone,L.Zaccaro,P.Di Lello,G.Digilio,S.Esposito, M.Saviano,B.Di Blasio,C.Pedone,P.V.Pedone,R.Fattorusso
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Key ref:
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C.Isernia
et al.
(2003).
NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein.
Chembiochem,
4,
171-180.
PubMed id:
DOI:
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Date:
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02-Jan-03
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Release date:
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04-Mar-03
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PROCHECK
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Headers
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References
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Q38895
(SUP_ARATH) -
Transcriptional regulator SUPERMAN from Arabidopsis thaliana
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Seq:
Struc:
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204 a.a.
38 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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DOI no:
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Chembiochem
4:171-180
(2003)
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PubMed id:
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NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein.
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C.Isernia,
E.Bucci,
M.Leone,
L.Zaccaro,
P.Di Lello,
G.Digilio,
S.Esposito,
M.Saviano,
B.Di Blasio,
C.Pedone,
P.V.Pedone,
R.Fattorusso.
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ABSTRACT
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Zinc finger domains of the classical type represent the most abundant DNA
binding domains in eukaryotic transcription factors. Plant proteins contain from
one to four zinc finger domains, which are characterized by high conservation of
the sequence QALGGH, shown to be critical for DNA-binding activity. The
Arabidopsis thaliana SUPERMAN protein, which contains a single QALGGH zinc
finger, is necessary for proper spatial development of reproductive floral
tissues and has been shown to specifically bind to DNA. Here, we report the
synthesis and UV and NMR spectroscopic structural characterization of a 37 amino
acid SUPERMAN region complexed to a Zn(2+) ion (Zn-SUP37) and present the first
high-resolution structure of a classical zinc finger domain from a plant
protein. The NMR structure of the SUPERMAN zinc finger domain consists of a very
well-defined betabetaalpha motif, typical of all other Cys(2)-His(2) zinc
fingers structurally characterized. As a consequence, the highly conserved
QALGGH sequence is located at the N terminus of the alpha helix. This region of
the domain of animal zinc finger proteins consists of hypervariable residues
that are responsible for recognizing the DNA bases. Therefore, we propose a
peculiar DNA recognition code for the QALGGH zinc finger domain that includes
all or some of the amino acid residues at positions -1, 2, and 3 (numbered
relative to the N terminus of the helix) and possibly others at the C-terminal
end of the recognition helix. This study further confirms that the zinc finger
domain, though very simple, is an extremely versatile DNA binding motif.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.Musumeci,
E.M.Bucci,
G.N.Roviello,
R.Sapio,
M.Valente,
M.Moccia,
M.E.Bianchi,
and
C.Pedone
(2011).
DNA-based strategies for blocking HMGB1 cytokine activity: design, synthesis and preliminary in vitro/in vivo assays of DNA and DNA-like duplexes.
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Mol Biosyst,
7,
1742-1752.
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I.Baglivo,
L.Russo,
S.Esposito,
G.Malgieri,
M.Renda,
A.Salluzzo,
B.Di Blasio,
C.Isernia,
R.Fattorusso,
and
P.V.Pedone
(2009).
The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains.
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Proc Natl Acad Sci U S A,
106,
6933-6938.
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J.Kam,
P.M.Gresshoff,
R.Shorter,
and
G.P.Xue
(2008).
The Q-type C2H2 zinc finger subfamily of transcription factors in Triticum aestivum is predominantly expressed in roots and enriched with members containing an EAR repressor motif and responsive to drought stress.
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Plant Mol Biol,
67,
305-322.
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G.Malgieri,
L.Russo,
S.Esposito,
I.Baglivo,
L.Zaccaro,
E.M.Pedone,
B.Di Blasio,
C.Isernia,
P.V.Pedone,
and
R.Fattorusso
(2007).
The prokaryotic Cys2His2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain.
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Proc Natl Acad Sci U S A,
104,
17341-17346.
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PDB code:
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R.Holmes-Davis,
G.Li,
A.C.Jamieson,
E.J.Rebar,
Q.Liu,
Y.Kong,
C.C.Case,
and
P.D.Gregory
(2005).
Gene regulation in planta by plant-derived engineered zinc finger protein transcription factors.
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Plant Mol Biol,
57,
411-423.
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Y.Uehara,
Y.Takahashi,
T.Berberich,
A.Miyazaki,
H.Takahashi,
K.Matsui,
M.Ohme-Takagi,
H.Saitoh,
R.Terauchi,
and
T.Kusano
(2005).
Tobacco ZFT1, a transcriptional repressor with a Cys2/His2 type zinc finger motif that functions in spermine-signaling pathway.
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Plant Mol Biol,
59,
435-448.
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C.C.Englbrecht,
H.Schoof,
and
S.Böhm
(2004).
Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome.
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BMC Genomics,
5,
39.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
