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PDBsum entry 1wid
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DNA binding protein PDB id
1wid

 

 

 

 

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Contents
Protein chain
117 a.a. *
* Residue conservation analysis
PDB id:
1wid
Name: DNA binding protein
Title: Solution structure of the b3 DNA-binding domain of rav1
Structure: DNA-binding protein rav1. Chain: a. Fragment: b3 DNA-binding domain. Synonym: transcription factor rav1. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: rav1. Other_details: cell-free synthesis
NMR struc: 20 models
Authors: K.Yamasaki,M.Inoue,T.Kigawa,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref: K.Yamasaki et al. (2004). Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1. Plant Cell, 16, 3448-3459. PubMed id: 15548737
Date:
28-May-04     Release date:   28-Nov-04    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9ZWM9  (RAV1_ARATH) -  AP2/ERF and B3 domain-containing transcription factor RAV1 from Arabidopsis thaliana
Seq:
Struc: 		344 a.a.
117 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Plant Cell 16:3448-3459 (2004)
PubMed id: 15548737  
 
 
Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1.
K.Yamasaki, T.Kigawa, M.Inoue, M.Tateno, T.Yamasaki, T.Yabuki, M.Aoki, E.Seki, T.Matsuda, Y.Tomo, N.Hayami, T.Terada, M.Shirouzu, T.Osanai, A.Tanaka, M.Seki, K.Shinozaki, S.Yokoyama.
 
  ABSTRACT  
 
The B3 DNA binding domain is shared amongst various plant-specific transcription factors, including factors involved in auxin-regulated and abscisic acid-regulated transcription. Herein, we report the NMR solution structure of the B3 domain of the Arabidopsis thaliana cold-responsive transcription factor RAV1. The structure consists of a seven-stranded open beta-barrel and two alpha-helices located at the ends of the barrel and is significantly similar to the structure of the noncatalytic DNA binding domain of the restriction enzyme EcoRII. An NMR titration experiment revealed a DNA recognition interface that enabled us to propose a structural model of the protein-DNA complex. The locations of the DNA-contacting residues are also likely to be similar to those of the EcoRII DNA binding domain.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20208064 K.Mochida, and K.Shinozaki (2010).
Genomics and bioinformatics resources for crop improvement.
  Plant Cell Physiol, 51, 497-523.  
19729506 D.Golovenko, E.Manakova, G.Tamulaitiene, S.Grazulis, and V.Siksnys (2009).
Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.
  Nucleic Acids Res, 37, 6613-6624.
PDB codes: 3hqf 3hqg
19503786 E.A.Romanel, C.G.Schrago, R.M.Couñago, C.A.Russo, and M.Alves-Ferreira (2009).
Evolution of the B3 DNA binding superfamily: new insights into REM family gene diversification.
  PLoS One, 4, e5791.  
  19255487 G.King, J.M.Hill, J.L.Martin, and J.S.Mylne (2009).
Expression, purification and preliminary X-ray diffraction studies of VERNALIZATION1(208-341) from Arabidopsis thaliana.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 291-294.  
19412652 M.Seki, and K.Shinozaki (2009).
Functional genomics using RIKEN Arabidopsis thaliana full-length cDNAs.
  J Plant Res, 122, 355-366.  
19400796 M.Szczepek, P.Mackeldanz, E.Möncke-Buchner, J.Alves, D.H.Krüger, and M.Reuter (2009).
Molecular analysis of restriction endonuclease EcoRII from Escherichia coli reveals precise regulation of its enzymatic activity by autoinhibition.
  Mol Microbiol, 72, 1011-1021.  
19478073 N.Mitsuda, and M.Ohme-Takagi (2009).
Functional analysis of transcription factors in Arabidopsis.
  Plant Cell Physiol, 50, 1232-1248.  
18987888 V.Gruber, S.Blanchet, A.Diet, O.Zahaf, A.Boualem, K.Kakar, B.Alunni, M.Udvardi, F.Frugier, and M.Crespi (2009).
Identification of transcription factors involved in root apex responses to salt stress in Medicago truncatula.
  Mol Genet Genomics, 281, 55-66.  
18346280 L.M.Iyer, S.Abhiman, and L.Aravind (2008).
MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases.
  Biol Direct, 3, 8.  
18476867 M.Santos-Mendoza, B.Dubreucq, S.Baud, F.Parcy, M.Caboche, and L.Lepiniec (2008).
Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis.
  Plant J, 54, 608-620.  
18470484 Q.Wang, Y.Guan, Y.Wu, H.Chen, F.Chen, and C.Chu (2008).
Overexpression of a rice OsDREB1F gene increases salt, drought, and low temperature tolerance in both Arabidopsis and rice.
  Plant Mol Biol, 67, 589-602.  
16977453 H.H.Marella, and R.S.Quatrano (2007).
The B2 domain of VIVIPAROUS1 is bi-functional and regulates nuclear localization and transactivation.
  Planta, 225, 863-872.  
17130173 M.M.Babu, L.M.Iyer, S.Balaji, and L.Aravind (2006).
The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons.
  Nucleic Acids Res, 34, 6505-6520.  
16492731 S.A.Braybrook, S.L.Stone, S.Park, A.Q.Bui, B.H.Le, R.L.Fischer, R.B.Goldberg, and J.J.Harada (2006).
Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis.
  Proc Natl Acad Sci U S A, 103, 3468-3473.  
16081658 J.K.Waltner, F.C.Peterson, B.L.Lytle, and B.F.Volkman (2005).
Structure of the B3 domain from Arabidopsis thaliana protein At1g16640.
  Protein Sci, 14, 2478-2483.
PDB code: 1yel
16252250 R.L.Rich, and D.G.Myszka (2005).
Survey of the year 2004 commercial optical biosensor literature.
  J Mol Recognit, 18, 431-478.  
16270233 R.Nag, M.K.Maity, and M.Dasgupta (2005).
Dual DNA binding property of ABA insensitive 3 like factors targeted to promoters responsive to ABA and auxin.
  Plant Mol Biol, 59, 821-838.  
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.  
16247004 S.Grazulis, E.Manakova, M.Roessle, M.Bochtler, G.Tamulaitiene, R.Huber, and V.Siksnys (2005).
Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.
  Proc Natl Acad Sci U S A, 102, 15797-15802.
PDB code: 2c1l
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 codes are shown on the right.

 

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