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PDBsum entry 2gli
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Transcription/DNA
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PDB id
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2gli
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Contents |
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* Residue conservation analysis
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DOI no:
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Science
261:1701-1707
(1993)
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PubMed id:
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Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers.
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N.P.Pavletich,
C.O.Pabo.
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ABSTRACT
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Zinc finger proteins, of the type first discovered in transcription factor IIIA
(TFIIIA), are one of the largest and most important families of DNA-binding
proteins. The crystal structure of a complex containing the five Zn fingers from
the human GLI oncogene and a high-affinity DNA binding site has been determined
at 2.6 A resolution. Finger one does not contact the DNA. Fingers two through
five bind in the major groove and wrap around the DNA, but lack the simple,
strictly periodic arrangement observed in the Zif268 complex. Fingers four and
five of GLI make extensive base contacts in a conserved nine base-pair region,
and this section of the DNA has a conformation intermediate between B-DNA and
A-DNA. Analyzing the GLI complex and comparing it with Zif268 offers new
perspectives on Zn finger-DNA recognition.
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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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R.Kothinti,
N.M.Tabatabai,
and
D.H.Petering
(2011).
Electrophoretic mobility shift assay of zinc finger proteins: competition for Zn(2+) bound to Sp1 in protocols including EDTA.
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J Inorg Biochem,
105,
569-576.
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A.N.Temiz,
P.V.Benos,
and
C.J.Camacho
(2010).
Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains.
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Nucleic Acids Res,
38,
2134-2144.
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A.Po,
E.Ferretti,
E.Miele,
E.De Smaele,
A.Paganelli,
G.Canettieri,
S.Coni,
L.Di Marcotullio,
M.Biffoni,
L.Massimi,
C.Di Rocco,
I.Screpanti,
and
A.Gulino
(2010).
Hedgehog controls neural stem cells through p53-independent regulation of Nanog.
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EMBO J,
29,
2646-2658.
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C.C.Chou,
Y.C.Lou,
T.K.Tang,
and
C.Chen
(2010).
Structure and DNA binding characteristics of the three-Cys(2)His(2) domain of mouse testis zinc finger protein.
|
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Proteins,
78,
2202-2212.
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E.Roessler,
and
M.Muenke
(2010).
The molecular genetics of holoprosencephaly.
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Am J Med Genet C Semin Med Genet,
154,
52-61.
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F.D.Urnov,
E.J.Rebar,
M.C.Holmes,
H.S.Zhang,
and
P.D.Gregory
(2010).
Genome editing with engineered zinc finger nucleases.
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Nat Rev Genet,
11,
636-646.
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H.S.Kang,
G.ZeRuth,
K.Lichti-Kaiser,
S.Vasanth,
Z.Yin,
Y.S.Kim,
and
A.M.Jetten
(2010).
Gli-similar (Glis) Krüppel-like zinc finger proteins: insights into their physiological functions and critical roles in neonatal diabetes and cystic renal disease.
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Histol Histopathol,
25,
1481-1496.
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M.Hatayama,
and
J.Aruga
(2010).
Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions.
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BMC Evol Biol,
10,
53.
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M.Winklmayr,
C.Schmid,
S.Laner-Plamberger,
A.Kaser,
F.Aberger,
T.Eichberger,
and
A.M.Frischauf
(2010).
Non-consensus GLI binding sites in Hedgehog target gene regulation.
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BMC Mol Biol,
11,
2.
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N.A.Temiz,
A.Trapp,
O.A.Prokopyev,
and
C.J.Camacho
(2010).
Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting.
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Bioinformatics,
26,
319-325.
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R.Iida,
M.Ueki,
and
T.Yasuda
(2010).
A novel transcriptional repressor, Rhit, is involved in heat-inducible and age-dependent expression of Mpv17-like protein, a participant in reactive oxygen species metabolism.
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Mol Cell Biol,
30,
2306-2315.
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R.Rohs,
X.Jin,
S.M.West,
R.Joshi,
B.Honig,
and
R.S.Mann
(2010).
Origins of specificity in protein-DNA recognition.
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Annu Rev Biochem,
79,
233-269.
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Y.Asaoka,
F.Kanai,
T.Ichimura,
K.Tateishi,
Y.Tanaka,
M.Ohta,
M.Seto,
M.Tada,
H.Ijichi,
T.Ikenoue,
T.Kawabe,
T.Isobe,
M.B.Yaffe,
and
M.Omata
(2010).
Identification of a suppressive mechanism for Hedgehog signaling through a novel interaction of Gli with 14-3-3.
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J Biol Chem,
285,
4185-4194.
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A.Barrallo-Gimeno,
and
M.A.Nieto
(2009).
Evolutionary history of the Snail/Scratch superfamily.
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Trends Genet,
25,
248-252.
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A.V.Persikov,
R.Osada,
and
M.Singh
(2009).
Predicting DNA recognition by Cys2His2 zinc finger proteins.
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Bioinformatics,
25,
22-29.
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E.Roessler,
F.Lacbawan,
C.Dubourg,
A.Paulussen,
J.Herbergs,
U.Hehr,
C.Bendavid,
N.Zhou,
M.Ouspenskaia,
S.Bale,
S.Odent,
V.David,
and
M.Muenke
(2009).
The full spectrum of holoprosencephaly-associated mutations within the ZIC2 gene in humans predicts loss-of-function as the predominant disease mechanism.
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Hum Mutat,
30,
E541-E554.
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Z.Yang,
H.J.Wen,
V.Minhas,
and
C.Wood
(2009).
The zinc finger DNA-binding domain of K-RBP plays an important role in regulating Kaposi's sarcoma-associated herpesvirus RTA-mediated gene expression.
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Virology,
391,
221-231.
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E.Kump,
J.Ji,
M.Wernli,
P.Häusermann,
and
P.Erb
(2008).
Gli2 upregulates cFlip and renders basal cell carcinoma cells resistant to death ligand-mediated apoptosis.
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Oncogene,
27,
3856-3864.
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F.Lu,
G.Li,
X.Cui,
C.Liu,
X.J.Wang,
and
X.Cao
(2008).
Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice.
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J Integr Plant Biol,
50,
886-896.
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J.Y.Beak,
H.S.Kang,
Y.S.Kim,
and
A.M.Jetten
(2008).
Functional analysis of the zinc finger and activation domains of Glis3 and mutant Glis3(NDH1).
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Nucleic Acids Res,
36,
1690-1702.
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K.J.Brayer,
and
D.J.Segal
(2008).
Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains.
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Cell Biochem Biophys,
50,
111-131.
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M.Hatayama,
T.Tomizawa,
K.Sakai-Kato,
P.Bouvagnet,
S.Kose,
N.Imamoto,
S.Yokoyama,
N.Utsunomiya-Tate,
K.Mikoshiba,
T.Kigawa,
and
J.Aruga
(2008).
Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain.
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Hum Mol Genet,
17,
3459-3473.
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PDB code:
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S.M.Shimeld
(2008).
C2H2 zinc finger genes of the Gli, Zic, KLF, SP, Wilms' tumour, Huckebein, Snail, Ovo, Spalt, Odd, Blimp-1, Fez and related gene families from Branchiostoma floridae.
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Dev Genes Evol,
218,
639-649.
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C.S.Merzdorf
(2007).
Emerging roles for zic genes in early development.
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Dev Dyn,
236,
922-940.
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B.Taneja,
A.Patel,
A.Slesarev,
and
A.Mondragón
(2006).
Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases.
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EMBO J,
25,
398-408.
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PDB codes:
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C.M.Yuen,
S.J.Rodda,
S.A.Vokes,
A.P.McMahon,
and
D.R.Liu
(2006).
Control of transcription factor activity and osteoblast differentiation in mammalian cells using an evolved small-molecule-dependent intein.
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J Am Chem Soc,
128,
8939-8946.
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O.Hallikas,
K.Palin,
N.Sinjushina,
R.Rautiainen,
J.Partanen,
E.Ukkonen,
and
J.Taipale
(2006).
Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity.
|
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Cell,
124,
47-59.
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W.Qiao,
M.Mooney,
A.J.Bird,
D.R.Winge,
and
D.J.Eide
(2006).
Zinc binding to a regulatory zinc-sensing domain monitored in vivo by using FRET.
|
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Proc Natl Acad Sci U S A,
103,
8674-8679.
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Y.Li,
X.Du,
F.Li,
Y.Deng,
Z.Yang,
Y.Wang,
Z.Pen,
Z.Wang,
W.Yuan,
C.Zhu,
and
X.Wu
(2006).
A novel zinc-finger protein ZNF436 suppresses transcriptional activities of AP-1 and SRE.
|
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Mol Biol Rep,
33,
287-294.
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C.Gaston-Massuet,
D.J.Henderson,
N.D.Greene,
and
A.J.Copp
(2005).
Zic4, a zinc-finger transcription factor, is expressed in the developing mouse nervous system.
|
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Dev Dyn,
233,
1110-1115.
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H.Saitsu,
M.Komada,
M.Suzuki,
R.Nakayama,
J.Motoyama,
K.Shiota,
and
M.Ishibashi
(2005).
Expression of the mouse Fgf15 gene is directly initiated by Sonic hedgehog signaling in the diencephalon and midbrain.
|
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Dev Dyn,
232,
282-292.
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N.Uchikoga,
S.Y.Takahashi,
R.Ke,
M.Sonoyama,
and
S.Mitaku
(2005).
Electric charge balance mechanism of extended soluble proteins.
|
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Protein Sci,
14,
74-80.
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Q.Tian,
H.Jin,
Y.Cui,
C.Guo,
and
X.Lu
(2005).
Regulation of Wnt gene expression.
|
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Dev Growth Differ,
47,
273-281.
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S.Durai,
M.Mani,
K.Kandavelou,
J.Wu,
M.H.Porteus,
and
S.Chandrasegaran
(2005).
Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.
|
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Nucleic Acids Res,
33,
5978-5990.
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V.Nguyen,
A.L.Chokas,
B.Stecca,
and
A.Ruiz i Altaba
(2005).
Cooperative requirement of the Gli proteins in neurogenesis.
|
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Development,
132,
3267-3279.
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Y.Chen,
S.D.Carrington-Lawrence,
P.Bai,
and
S.K.Weller
(2005).
Mutations in the putative zinc-binding motif of UL52 demonstrate a complex interdependence between the UL5 and UL52 subunits of the human herpes simplex virus type 1 helicase/primase complex.
|
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J Virol,
79,
9088-9096.
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A.Dahlén,
C.D.Fletcher,
F.Mertens,
J.A.Fletcher,
A.R.Perez-Atayde,
M.J.Hicks,
M.Debiec-Rychter,
R.Sciot,
J.Wejde,
R.Wedin,
N.Mandahl,
and
I.Panagopoulos
(2004).
Activation of the GLI oncogene through fusion with the beta-actin gene (ACTB) in a group of distinctive pericytic neoplasms: pericytoma with t(7;12).
|
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Am J Pathol,
164,
1645-1653.
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H.Jafar-Nejad,
H.J.Bellen,
and
H.J.Bellen
(2004).
Gfi/Pag-3/senseless zinc finger proteins: a unifying theme?
|
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Mol Cell Biol,
24,
8803-8812.
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J.M.Vitolo,
Z.Yang,
R.Basavappa,
and
J.J.Hayes
(2004).
Structural features of transcription factor IIIA bound to a nucleosome in solution.
|
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Mol Cell Biol,
24,
697-707.
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M.J.Lachenmann,
J.E.Ladbury,
X.Qian,
K.Huang,
R.Singh,
and
M.A.Weiss
(2004).
Solvation and the hidden thermodynamics of a zinc finger probed by nonstandard repair of a protein crevice.
|
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Protein Sci,
13,
3115-3126.
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PDB code:
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A.J.Bird,
K.McCall,
M.Kramer,
E.Blankman,
D.R.Winge,
and
D.J.Eide
(2003).
Zinc fingers can act as Zn2+ sensors to regulate transcriptional activation domain function.
|
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EMBO J,
22,
5137-5146.
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A.T.Hamilton,
S.Huntley,
J.Kim,
E.Branscomb,
and
L.Stubbs
(2003).
Lineage-specific expansion of KRAB zinc-finger transcription factor genes: implications for the evolution of vertebrate regulatory networks.
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Cold Spring Harb Symp Quant Biol,
68,
131-140.
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H.N.Arst,
and
M.A.Peñalva
(2003).
pH regulation in Aspergillus and parallels with higher eukaryotic regulatory systems.
|
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Trends Genet,
19,
224-231.
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Y.S.Kim,
G.Nakanishi,
M.Lewandoski,
and
A.M.Jetten
(2003).
GLIS3, a novel member of the GLIS subfamily of Krüppel-like zinc finger proteins with repressor and activation functions.
|
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Nucleic Acids Res,
31,
5513-5525.
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H.L.Ng,
and
R.E.Dickerson
(2002).
Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG.
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Nucleic Acids Res,
30,
4061-4067.
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H.Nishida
(2002).
Patterning the marginal zone of early ascidian embryos: localized maternal mRNA and inductive interactions.
|
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Bioessays,
24,
613-624.
|
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M.Persson,
D.Stamataki,
P.te Welscher,
E.Andersson,
J.Böse,
U.Rüther,
J.Ericson,
and
J.Briscoe
(2002).
Dorsal-ventral patterning of the spinal cord requires Gli3 transcriptional repressor activity.
|
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Genes Dev,
16,
2865-2878.
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N.Dathan,
L.Zaccaro,
S.Esposito,
C.Isernia,
J.G.Omichinski,
A.Riccio,
C.Pedone,
B.Di Blasio,
R.Fattorusso,
and
P.V.Pedone
(2002).
The Arabidopsis SUPERMAN protein is able to specifically bind DNA through its single Cys2-His2 zinc finger motif.
|
| |
Nucleic Acids Res,
30,
4945-4951.
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B.Gebelein,
and
R.Urrutia
(2001).
Sequence-specific transcriptional repression by KS1, a multiple-zinc-finger-Krüppel-associated box protein.
|
| |
Mol Cell Biol,
21,
928-939.
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C.O.Pabo,
E.Peisach,
and
R.A.Grant
(2001).
Design and selection of novel Cys2His2 zinc finger proteins.
|
| |
Annu Rev Biochem,
70,
313-340.
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C.W.Garvie,
and
C.Wolberger
(2001).
Recognition of specific DNA sequences.
|
| |
Mol Cell,
8,
937-946.
|
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D.P.Giedroc,
X.Chen,
and
J.L.Apuy
(2001).
Metal response element (MRE)-binding transcription factor-1 (MTF-1): structure, function, and regulation.
|
| |
Antioxid Redox Signal,
3,
577-596.
|
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M.J.Smith,
S.D.Gitlin,
C.M.Browning,
B.R.Lane,
N.M.Clark,
N.Shah,
S.Rainier,
and
D.M.Markovitz
(2001).
GLI-2 modulates retroviral gene expression.
|
| |
J Virol,
75,
2301-2313.
|
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M.Nagaoka,
T.Kaji,
M.Imanishi,
Y.Hori,
W.Nomura,
and
Y.Sugiura
(2001).
Multiconnection of identical zinc finger: implication for DNA binding affinity and unit modulation of the three zinc finger domain.
|
| |
Biochemistry,
40,
2932-2941.
|
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R.D.Knight,
and
S.M.Shimeld
(2001).
Identification of conserved C2H2 zinc-finger gene families in the Bilateria.
|
| |
Genome Biol,
2,
RESEARCH0016.
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Y.Uno,
K.Matsushita,
M.Nagaoka,
and
Y.Sugiura
(2001).
Finger-positional change in three zinc finger protein Sp1: influence of terminal finger in DNA recognition.
|
| |
Biochemistry,
40,
1787-1795.
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A.Hata,
J.Seoane,
G.Lagna,
E.Montalvo,
A.Hemmati-Brivanlou,
and
J.Massagué
(2000).
OAZ uses distinct DNA- and protein-binding zinc fingers in separate BMP-Smad and Olf signaling pathways.
|
| |
Cell,
100,
229-240.
|
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B.Wang,
J.F.Fallon,
and
P.A.Beachy
(2000).
Hedgehog-regulated processing of Gli3 produces an anterior/posterior repressor gradient in the developing vertebrate limb.
|
| |
Cell,
100,
423-434.
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E.H.Villavicencio,
D.O.Walterhouse,
and
P.M.Iannaccone
(2000).
The sonic hedgehog-patched-gli pathway in human development and disease.
|
| |
Am J Hum Genet,
67,
1047-1054.
|
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E.T.Young,
N.Kacherovsky,
and
C.Cheng
(2000).
An accessory DNA binding motif in the zinc finger protein Adr1 assists stable binding to DNA and can be replaced by a third finger.
|
| |
Biochemistry,
39,
567-574.
|
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J.H.Laity,
H.J.Dyson,
and
P.E.Wright
(2000).
Molecular basis for modulation of biological function by alternate splicing of the Wilms' tumor suppressor protein.
|
| |
Proc Natl Acad Sci U S A,
97,
11932-11935.
|
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J.M.Matthews,
K.Kowalski,
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EMBO J,
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Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb.
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Nat Struct Biol,
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PDB codes:
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L.Shimoni,
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Hydrogen bonding motifs of protein side chains: descriptions of binding of arginine and amide groups.
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Protein Sci,
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Nucleic Acids Res,
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M.Abrink,
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Isolation of cDNA clones for 42 different Krüppel-related zinc finger proteins expressed in the human monoblast cell line U-937.
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DNA Cell Biol,
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Sequence-specific DNA binding by covalently constrained peptide dimers of the basic leucine zipper protein GCN4.
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Nucleic Acids Res,
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YY1 facilitates the association of serum response factor with the c-fos serum response element.
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Mol Cell Biol,
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S.Sun
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BZP, a novel serum-responsive zinc finger protein that inhibits gene transcription.
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Mol Cell Biol,
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The Ikaros gene encodes a family of functionally diverse zinc finger DNA-binding proteins.
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Mol Cell Biol,
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Identification of potential target genes for Adr1p through characterization of essential nucleotides in UAS1.
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Mol Cell Biol,
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Regulatory rearrangements and smg-sensitive alleles of the C. elegans sex-determining gene tra-1.
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Characterization of the DNA-binding properties of the myeloid zinc finger protein MZF1: two independent DNA-binding domains recognize two DNA consensus sequences with a common G-rich core.
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Mol Cell Biol,
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| |
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PDB codes:
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L.Nekludova,
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Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes.
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Proc Natl Acad Sci U S A,
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Requirement for a zinc motif for template recognition by the bacteriophage T7 primase.
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A factor that regulates the class II major histocompatibility complex gene DPA is a member of a subfamily of zinc finger proteins that includes a Drosophila developmental control protein.
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Mol Cell Biol,
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M.Suzuki,
M.Gerstein,
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Stereochemical basis of DNA recognition by Zn fingers.
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Molecular cloning of a novel human cDNA encoding a zinc finger protein that binds to the interleukin-3 promoter.
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Proc Natl Acad Sci U S A,
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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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