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2  structures 101  species 0  interactions 2169  sequences 44  architectures

Family: B3 (PF02362)

Summary: B3 DNA binding domain

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B3 domain Edit Wikipedia article

B3 DNA binding domain
B3Domain 1WID.png
B3 DNA binding domain of RAV1
Identifiers
Symbol B3_domain
Pfam PF02362
InterPro IPR003340
PROSITE PS50863
SCOP 1wid
SUPERFAMILY 1wid

The B3 DNA binding domain (DBD) is a highly conserved domain found exclusively in transcription factors, from higher plants (≥40 species) (Pfam PF02362) combined with other domains (IPR003340). It consists of 100-120 residues, includes seven beta strands and two alpha helices that form a DNA-binding pseudobarrel protein fold (SCOP 117343); it interacts with the major groove of DNA.[1]

B3 families[edit]

In Arabidopsis thaliana, there are three main families of transcription factors that contain B3 domain:[2]

protein ARF1-B3 ABI3-B3 RAV1-B3
B3 structure derived by molecular model[1] molecular model[1] NMR[1]
B3 recognition sequence TGTCTC[3][4] CATGCA[5][6] CACCTG[7]

PDB 1WID[1] and PDB 1YEL[8] are only known NMR solution phase structures of the B3 DNA Binding Domain.

Related proteins[edit]

The N-terminal domain of restriction endonuclease EcoRII; the C-terminal domain of restriction endonuclease BfiI possess a similar DNA-binding pseudobarrel protein fold.[9][10]

See also[edit]

References[edit]

  1. ^ a b c d e Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S (2004). "Solution Structure of the B3 DNA Binding Domain of the Arabidopsis Cold-Responsive Transcription Factor RAV1". Plant Cell 16 (12): 3448–59. doi:10.1105/tpc.104.026112. PMC 535885. PMID 15548737. 
  2. ^ Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu G (2000). "Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes". Science 290 (5499): 2105–10. doi:10.1126/science.290.5499.2105. PMID 11118137. 
  3. ^ Ulmasov T, Hagen G, Guilfoyle TJ (1997). "ARF1, a transcription factor that binds to auxin response elements". Science 276 (5320): 1865–8. doi:10.1126/science.276.5320.1865. PMID 9188533. 
  4. ^ Tiwari SB, Hagen G, Guilfoyle TJ (2003). "The Roles of Auxin Response Factor Domains in Auxin-Responsive Transcription". Plant Cell 15 (2): 533–43. doi:10.1105/tpc.008417. PMC 141219. PMID 12566590. 
  5. ^ Suzuki M, Kao CY, McCarty DR (1997). "The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity". Plant Cell 9 (5): 799–807. doi:10.1105/tpc.9.5.799. PMC 156957. PMID 9165754. 
  6. ^ Ezcurra I, Wycliffe P, Nehlin L, Ellerström M, Rask L (2000). "Transactivation of the Brassica napus napin promoter by ABI3 requires interaction of the conserved B2 and B3 domains of ABI3 with different cis-elements: B2 mediates activation through an ABRE, whereas B3 interacts with an RY/G-box". Plant J. 24 (1): 57–66. doi:10.1046/j.1365-313x.2000.00857.x. PMID 11029704. 
  7. ^ Kagaya Y, Ohmiya K, Hattori T (1999). "RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants". Nucleic Acids Res. 27 (2): 470–8. doi:10.1093/nar/27.2.470. PMC 148202. PMID 9862967. 
  8. ^ Waltner, J.K., Peterson, F.C., Lytle, B.L., Volkman, B.F. (2005). "Structure of the B3 domain from Arabidopsis thaliana protein At1g16640". Protein Sci 14 (9): 2478–83. doi:10.1110/ps.051606305. PMC 2253459. PMID 16081658. 
  9. ^ Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L (2004). "Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold". J. Mol. Biol. 335 (1): 307–19. doi:10.1016/j.jmb.2003.10.030. PMID 14659759. 
  10. ^ Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V (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 (44): 15797–802. doi:10.1073/pnas.0507949102. PMC 1266039. PMID 16247004. 

External links[edit]

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

B3 DNA binding domain Provide feedback

This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in [1] this domain is found in VP1/AB13 transcription factors [2]. Some proteins also have a second AP2 DNA binding domain PF00847 such as RAV1 Q9ZWM9 [1]. DNA binding activity was demonstrated by [3].

Literature references

  1. Kagaya Y, Ohmiya K, Hattori T; , Nucleic Acids Res 1999;27:470-478.: RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. PUBMED:9862967 EPMC:9862967

  2. Ulmasov T, Hagen G, Guilfoyle TJ; , Science 1997;276:1865-1868.: ARF1, a transcription factor that binds to auxin response elements. PUBMED:9188533 EPMC:9188533

  3. Suzuki M, Kao CY, McCarty DR; , Plant Cell 1997;9:799-807.: The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity. PUBMED:9165754 EPMC:9165754


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003340

Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors [PUBMED:9862967]. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [PUBMED:9862967].

This entry represents the B3 DNA binding domain. Its DNA binding activity has been demonstrated [PUBMED:9165754]. The B3 domain can be found in one or more copies.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan DNA_b-psBarrel (CL0405), which contains the following 3 members:

B3 DUF313 EcoRII-N

Alignments

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(746)
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  Seed
(114)
Full
(2169)
Representative proteomes NCBI
(2264)
Meta
(0)
RP15
(219)
RP35
(746)
RP55
(1021)
RP75
(1310)
Alignment:
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  Seed
(114)
Full
(2169)
Representative proteomes NCBI
(2264)
Meta
(0)
RP15
(219)
RP35
(746)
RP55
(1021)
RP75
(1310)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_582 (release 5.2)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 114
Number in full: 2169
Average length of the domain: 98.00 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 23.90 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.1 30.1
Trusted cut-off 30.1 30.1
Noise cut-off 29.9 30.0
Model length: 100
Family (HMM) version: 16
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Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the B3 domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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