PDBsum entry 3gcc

Transcription factor

PDB id

3gcc

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Contents

			Protein chain

					63 a.a. *

* Residue conservation analysis

PDB id:

3gcc

Links
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Name:

Transcription factor

Title:

Solution structure of the gcc-box binding domain, nmr, 46 structures

Structure:

Aterf1. Chain: a. Fragment: gcc-box binding domain. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Cell_line: bl21. Gene: aterf1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: DNA-binding domain of aterf1

NMR struc:

46 models

Authors:

M.D.Allen,K.Yamasaki,M.Ohme-Takagi,M.Tateno,M.Suzuki

Key ref:

M.D.Allen et al. (1998). A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. Embo J, 17, 5484-5496. PubMed id: 9736626 DOI: 10.1093/emboj/17.18.5484

Date:

13-Mar-98

Release date:

23-Mar-99

PROCHECK

	Headers

	References

Protein chain

O80337 (EF100_ARATH) - Ethylene-responsive transcription factor 1A from Arabidopsis thaliana

Seq: Struc:					268 a.a. 63 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.?

[IntEnz] [ExPASy] [KEGG] [BRENDA]

DOI no: 10.1093/emboj/17.18.5484	Embo J 17:5484-5496 (1998)
PubMed id: 9736626

A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.
M.D.Allen, K.Yamasaki, M.Ohme-Takagi, M.Tateno, M.Suzuki.

ABSTRACT

The 3D solution structure of the GCC-box binding domain of a protein from Arabidopsis thaliana in complex with its target DNA fragment has been determined by heteronuclear multidimensional NMR in combination with simulated annealing and restrained molecular dynamic calculation. The domain consists of a three-stranded anti-parallel beta-sheet and an alpha-helix packed approximately parallel to the beta-sheet. Arginine and tryptophan residues in the beta-sheet are identified to contact eight of the nine consecutive base pairs in the major groove, and at the same time bind to the sugar phosphate backbones. The target DNA bends slightly at the central CG step, thereby allowing the DNA to follow the curvature of the beta-sheet.

Selected figure(s)



	Figure 2. Figure 2 Comparison of GBD with a zinc finger. (A) Superposition of the backbones of 46 GBD structures, Lys145-Val206, in the absence of the DNA refined by simulated annealing. Different colors are used for indicating the secondary structural elements. The N- and C-termini are labeled. (B) A diagrammatic drawing of the final structure made by energy minimization of the mean co-ordinates of the ensemble shown in (A), superimposed on a presentation of electropolarization. Positive charges are shown in blue and negative charges in red. The side that recognizes DNA is indicated with an arrow. (C) The 3D structure and electropolarization of the first zinc finger of SWI5 (Protein Data Bank code 1NCS) shown in the same way as in (B).		Figure 5. Figure 5 Contacts between GBD and the GCC-box. (A) A stereo subfigure of part of the GBD -DNA complex structure. The contacts are indicated by broken lines with different colors; green for hydrogen bonds and yellow for ionic contacts. Different colors are used for the coding (crimson) and complementary (cyan) strands. (B) A diagrammatic representation of the contacts identified after restrained molecular dynamic calculation. The DNA is drawn by looking into the major groove. Yellow circles represent the phosphate groups. The contacted bases are highlighted in cyan. The same color code as in (A) is used for typing the contacts and, in addition, brown for hydrophobic contacts. The distance between Glu160 and C19 is slightly larger than the standard hydrogen bonding distance (shown by a broken line). The up -down transcription direction is indicated. The coding and complementary strands are labeled. Gd: guanidyl group. (C) A diagrammatic representation of the NOEs observed between amino acid residues and the target DNA. The bases with which the NOEs are observed are highlighted in orange. (D) The three stranded -sheet of GBD. Residues are colored differently depending on the function; base-contacting only (blue), backbone-binding only (yellow) and having both functions (green). An ellipsoid is drawn by connecting the green positions, which is divided into two halves by the broken line that crosses Ala159. The CG step is highlighted in cyan. The up -down transcription direction is indicated. The coding and complementary strands are labeled. (E) A two stranded -sheet of the MetJ -Arc type. The figure was made using the co-ordinates of the MetJ -DNA complex (Protein Data Base code 1CMA). The six amino acid positions used for base recognition by the MetJ -Arc family are in blue. An ellipsoid is drawn enclosing the blue residues. Compare the ellipsoid with the larger ellipsoid shown in (D) for an appreciation of the difference in size of the two interaction sites.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21169347

A.M.Sharoni, M.Nuruzzaman, K.Satoh, T.Shimizu, H.Kondoh, T.Sasaya, I.R.Choi, T.Omura, and S.Kikuchi (2011).
Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice.

Plant Cell Physiol, 52, 344-360.

21274560

M.Wisniewski, J.Norelli, C.Bassett, T.Artlip, and D.Macarisin (2011).
Ectopic expression of a novel peach (Prunus persica) CBF transcription factor in apple (Malus × domestica) results in short-day induced dormancy and increased cold hardiness.

Planta, 233, 971-983.

21127996

X.Wang, X.Chen, Y.Liu, H.Gao, Z.Wang, and G.Sun (2011).
CkDREB gene in Caragana korshinskii is involved in the regulation of stress response to multiple abiotic stresses as an AP2/EREBP transcription factor.

Mol Biol Rep, 38, 2801-2811.

20922546

M.K.Sharma, R.Kumar, A.U.Solanke, R.Sharma, A.K.Tyagi, and A.K.Sharma (2010).
Identification, phylogeny, and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato.

Mol Genet Genomics, 284, 455-475.

21143675

M.Y.Chung, J.Vrebalov, R.Alba, J.Lee, R.McQuinn, J.D.Chung, P.Klein, and J.Giovannoni (2010).
A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening.

Plant J, 64, 936-947.

20233336

R.Quan, S.Hu, Z.Zhang, H.Zhang, Z.Zhang, and R.Huang (2010).
Overexpression of an ERF transcription factor TSRF1 improves rice drought tolerance.

Plant Biotechnol J, 8, 476-488.

20144952

S.Campagne, O.Saurel, V.Gervais, and A.Milon (2010).
Structural determinants of specific DNA-recognition by the THAP zinc finger.

Nucleic Acids Res, 38, 3466-3476.

PDB code:

2ko0

19913037

S.E.Lindner, E.K.De Silva, J.L.Keck, and M.Llinás (2010).
Structural determinants of DNA binding by a P. falciparum ApiAP2 transcriptional regulator.

J Mol Biol, 395, 558-567.

PDB code:

3igm

20657661

S.F.Altschul, J.C.Wootton, E.Zaslavsky, and Y.K.Yu (2010).
The construction and use of log-odds substitution scores for multiple sequence alignment.

PLoS Comput Biol, 6, e1000852.

21041975

X.Wang, X.Chen, Z.Wang, D.Nikolay, C.Vladimir, and H.Gao (2010).
Isolation and characterization of GoDREB encoding an ERF-type protein in forage legume Galegae orientalis.

Genes Genet Syst, 85, 157-166.

19523101

A.Champion, E.Hebrard, B.Parra, C.Bournaud, P.Marmey, C.Tranchant, and M.Nicole (2009).
Molecular diversity and gene expression of cotton ERF transcription factors reveal that group IXa members are responsive to jasmonate, ethylene and Xanthomonas.

Mol Plant Pathol, 10, 471-485.

19145605

A.L.Stewart, and M.L.Waters (2009).
Structural effects on ss- and dsDNA recognition by a beta-hairpin peptide.

Chembiochem, 10, 539-544.

19737930

A.Szwagierczak, U.Antonenka, G.M.Popowicz, T.Sitar, T.A.Holak, and A.Rakin (2009).
Structures of the arm-type binding domains of HPI and HAI7 integrases.

J Biol Chem, 284, 31664-31671.

PDB codes:

3jtz 3ju0

19324050

E.A.Fadeev, M.D.Sam, and R.T.Clubb (2009).
NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove.

J Mol Biol, 388, 682-690.

PDB code:

2wcc

19457981

M.Navarro, G.Marque, C.Ayax, G.Keller, J.P.Borges, C.Marque, and C.Teulières (2009).
Complementary regulation of four Eucalyptus CBF genes under various cold conditions.

J Exp Bot, 60, 2713-2724.

19478073

N.Mitsuda, and M.Ohme-Takagi (2009).
Functional analysis of transcription factors in Arabidopsis.

Plant Cell Physiol, 50, 1232-1248.

17922220

Y.Yang, J.Wu, K.Zhu, L.Liu, F.Chen, and D.Yu (2009).
Identification and characterization of two chrysanthemum (Dendronthema x moriforlium) DREB genes, belonging to the AP2/EREBP family.

Mol Biol Rep, 36, 71-81.

18317935

A.K.Knox, C.Li, A.Vágújfalvi, G.Galiba, E.J.Stockinger, and J.Dubcovsky (2008).
Identification of candidate CBF genes for the frost tolerance locus Fr-Am2 in Triticum monococcum.

Plant Mol Biol, 67, 257-270.

18832187

G.Zhang, M.Chen, X.Chen, Z.Xu, S.Guan, L.C.Li, A.Li, J.Guo, L.Mao, and Y.Ma (2008).
Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.).

J Exp Bot, 59, 4095-4107.

18713346

L.Wang, Y.Luo, L.Zhang, J.Zhao, Z.Hu, Y.Fan, and C.Zhang (2008).
Isolation and characterization of a C-repeat binding transcription factor from maize.

J Integr Plant Biol, 50, 965-974.

18089556

S.Sun, J.P.Yu, F.Chen, T.J.Zhao, X.H.Fang, Y.Q.Li, and S.F.Sui (2008).
TINY, a dehydration-responsive element (DRE)-binding protein-like transcription factor connecting the DRE- and ethylene-responsive element-mediated signaling pathways in Arabidopsis.

J Biol Chem, 283, 6261-6271.

18316719

S.Taketa, S.Amano, Y.Tsujino, T.Sato, D.Saisho, K.Kakeda, M.Nomura, T.Suzuki, T.Matsumoto, K.Sato, H.Kanamori, S.Kawasaki, and K.Takeda (2008).
Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway.

Proc Natl Acad Sci U S A, 105, 4062-4067.

17160455

H.Zhang, W.Li, J.Chen, Y.Yang, Z.Zhang, H.Zhang, X.C.Wang, and R.Huang (2007).
Transcriptional activator TSRF1 reversely regulates pathogen resistance and osmotic stress tolerance in tobacco.

Plant Mol Biol, 63, 63-71.

17136305

J.G.Liu, Z.Zhang, Q.L.Qin, R.H.Peng, A.S.Xiong, J.M.Chen, F.Xu, H.Zhu, and Q.H.Yao (2007).
Isolated and characterization of a cDNA encoding ethylene-responsive element binding protein (EREBP)/AP2-type protein, RCBF2, in Oryza sativa L.

Biotechnol Lett, 29, 165-173.

17488240

K.Sasaki, I.Mitsuhara, S.Seo, H.Ito, H.Matsui, and Y.Ohashi (2007).
Two novel AP2/ERF domain proteins interact with cis-element VWRE for wound-induced expression of the Tobacco tpoxN1 gene.

Plant J, 50, 1079-1092.

17285309

M.Badawi, J.Danyluk, B.Boucho, M.Houde, and F.Sarhan (2007).
The CBF gene family in hexaploid wheat and its relationship to the phylogenetic complexity of cereal CBFs.

Mol Genet Genomics, 277, 533-554.

17541631

N.Liu, N.Q.Zhong, G.L.Wang, L.J.Li, X.L.Liu, Y.K.He, and G.X.Xia (2007).
Cloning and functional characterization of PpDBF1 gene encoding a DRE-binding transcription factor from Physcomitrella patens.

Planta, 226, 827-838.

17639404

Y.Li, B.Zhu, W.Xu, H.Zhu, A.Chen, Y.Xie, Y.Shao, and Y.Luo (2007).
LeERF1 positively modulated ethylene triple response on etiolated seedling, plant development and fruit ripening and softening in tomato.

Plant Cell Rep, 26, 1999-2008.

16429262

C.P.Song, and D.W.Galbraith (2006).
AtSAP18, an orthologue of human SAP18, is involved in the regulation of salt stress and mediates transcriptional repression in Arabidopsis.

Plant Mol Biol, 60, 241-257.

16545065

H.Duan, F.Li, X.Wu, D.Ma, M.Wang, and Y.Hou (2006).
Cloning and characterization of two EREBP transcription factors from cotton (Gossypium hirsutum L.).

Biochemistry (Mosc), 71, 285-293.

16809858

J.Qin, K.Zuo, J.Zhao, H.Ling, Y.Cao, C.Qiu, F.Li, X.Sun, and K.Tang (2006).
Overexpression of GbERF confers alteration of ethylene-responsive gene expression and enhanced resistance to Pseudomonas syringae in transgenic tobacco.

J Biosci, 31, 255-263.

16505376

M.O.Lindberg, E.Haglund, I.A.Hubner, E.I.Shakhnovich, and M.Oliveberg (2006).
Identification of the minimal protein-folding nucleus through loop-entropy perturbations.

Proc Natl Acad Sci U S A, 103, 4083-4088.

17096212

N.Marsch-Martinez, R.Greco, J.D.Becker, S.Dixit, J.H.Bergervoet, A.Karaba, S.de Folter, and A.Pereira (2006).
BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways.

Plant Mol Biol, 62, 825-843.

16970618

G.Yi, J.H.Choi, E.G.Jeong, N.S.Chon, K.K.Jena, Y.C.Ku, D.H.Kim, M.Y.Eun, J.S.Jeon, and M.H.Nam (2005).
Morphological and molecular characterization of a new frizzy panicle mutant, "fzp-9(t)", in rice (Oryza sativa L.).

Hereditas, 142, 92-97.

16307362

J.X.Feng, D.Liu, Y.Pan, W.Gong, L.G.Ma, J.C.Luo, X.W.Deng, and Y.X.Zhu (2005).
An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness of the Arabidopsis AP2/EREBP transcription factor gene family.

Plant Mol Biol, 59, 853-868.

16040597

S.Balaji, M.M.Babu, L.M.Iyer, and L.Aravind (2005).
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains.

Nucleic Acids Res, 33, 3994-4006.

16314321

T.C.Galvão, and J.O.Thomas (2005).
Structure-specific binding of MeCP2 to four-way junction DNA through its methyl CpG-binding domain.

Nucleic Acids Res, 33, 6603-6609.

15083810

H.A.Ernst, A.N.Olsen, S.Larsen, and L.Lo Leggio (2004).
Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors.

EMBO Rep, 5, 297-303.

PDB codes:

1ut4 1ut7

12655002

B.A.Krizek (2003).
AINTEGUMENTA utilizes a mode of DNA recognition distinct from that used by proteins containing a single AP2 domain.

Nucleic Acids Res, 31, 1859-1868.

12682016

S.X.Cohen, M.Moulin, S.Hashemolhosseini, K.Kilian, M.Wegner, and C.W.Müller (2003).
Structure of the GCM domain-DNA complex: a DNA-binding domain with a novel fold and mode of target site recognition.

EMBO J, 22, 1835-1845.

PDB code:

1odh

12914659

W.W.Li, G.B.Quinn, N.N.Alexandrov, P.E.Bourne, and I.N.Shindyalov (2003).
A comparative proteomics resource: proteins of Arabidopsis thaliana.

Genome Biol, 4, R51.

12475496

B.C.Lam, and E.Blumwald (2002).
Domains as functional building blocks of plant proteins.

Trends Plant Sci, 7, 544-549.

11904406

J.M.Wojciak, D.Sarkar, A.Landy, and R.T.Clubb (2002).
Arm-site binding by lambda -integrase: solution structure and functional characterization of its amino-terminal domain.

Proc Natl Acad Sci U S A, 99, 3434-3439.

PDB code:

1kjk

11741530

C.W.Garvie, and C.Wolberger (2001).
Recognition of specific DNA sequences.

Mol Cell, 8, 937-946.

11371345

I.Ohki, N.Shimotake, N.Fujita, J.Jee, T.Ikegami, M.Nakao, and M.Shirakawa (2001).
Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA.

Cell, 105, 487-497.

PDB code:

1ig4

11440157

T.Koyama, S.Kitajima, and F.Sato (2001).
Expression of PR-5d and ERF genes in cultured tobacco cells and their NaCl stress-response.

Biosci Biotechnol Biochem, 65, 1270-1273.

11600698

Y.Nagano, H.Furuhashi, T.Inaba, and Y.Sasaki (2001).
A novel class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences.

Nucleic Acids Res, 29, 4097-4105.

11118137

J.L.Riechmann, J.Heard, G.Martin, L.Reuber, C.Jiang, J.Keddie, L.Adam, O.Pineda, O.J.Ratcliffe, R.R.Samaha, R.Creelman, M.Pilgrim, P.Broun, J.Z.Zhang, D.Ghandehari, B.K.Sherman, and G.Yu (2000).
Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.

Science, 290, 2105-2110.

11058102

S.Nole-Wilson, and B.A.Krizek (2000).
DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA.

Nucleic Acids Res, 28, 4076-4082.

10368306

T.Darden, L.Perera, L.Li, and L.Pedersen (1999).
New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations.

Structure, 7, R55-R60.

10607299

V.K.Thara, X.Tang, Y.Q.Gu, G.B.Martin, and J.M.Zhou (1999).
Pseudomonas syringae pv tomato induces the expression of tomato EREBP-like genes pti4 and pti5 independent of ethylene, salicylate and jasmonate

Plant J, 20, 475-483.

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.