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0  structures 114  species 0  interactions 842  sequences 14  architectures

Family: BEN (PF10523)

Summary: BEN domain

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BEN domain Edit Wikipedia article

BEN
Identifiers
Symbol BEN
Pfam PF10523
InterPro IPR018379

In molecular biology, the BEN domain is protein domain is found in diverse proteins including:

  • SMAR1 (Scaffold/Matrix attachment region-binding protein 1; also known as BANP), a tumour-suppressor MAR-binding protein that down-regulates Cyclin D1 expression by recruiting HDAC1-mSin3A co-repressor complex at Cyclin D1 promoter locus; SMAR1 is the target of prostaglandin A2 (PGA2) induced growth arrest.[1][2]
  • NACC1, a novel member of the POZ/BTB (Pox virus and Zinc finger/Bric-a-bracTramtrack Broad complex), but which varies from other proteins of this class in that it lacks the characteristic DNA-binding motif.[3]
  • E5R protein from Chordopoxvirus virosomes, which is found in cytoplasmic sites of viral DNA replication.[5]
  • Several proteins of polydnaviruses.

The BEN domain is predicted to function as an adaptor for the higher-order structuring of chromatin, and recruitment of chromatin modifying factors in transcriptional regulation. It has been suggested to mediate protein-DNA and protein-protein interactions during chromatin organisation and transcription. The presence of BEN domains in a poxviral early virosomal protein and in polydnaviral proteins also suggests a possible role in the organisation of viral DNA during replication or transcription. They are generally linked to other globular domains with functions related to transcriptional regulation and chromatin structure, such as BTB, C4DM, and C2H2 fingers.[6]

This domain is predicted to form an all-alpha fold with four conserved helices. Its conservation pattern revealed several conserved residues, most of which have hydrophobic side-chains and are likely to stabilise the fold through helix-helix packing.[6]

References

  1. ^ Rampalli S, Pavithra L, Bhatt A, Kundu TK, Chattopadhyay S (October 2005). "Tumor suppressor SMAR1 mediates cyclin D1 repression by recruitment of the SIN3/histone deacetylase 1 complex". Mol. Cell. Biol. 25 (19): 8415–29. doi:10.1128/MCB.25.19.8415-8429.2005. PMC 1265755. PMID 16166625. 
  2. ^ Pavithra L, Rampalli S, Sinha S, Sreenath K, Pestell RG, Chattopadhyay S (2007). "Stabilization of SMAR1 mRNA by PGA2 involves a stem loop structure in the 5' UTR". Nucleic Acids Res. 35 (18): 6004–16. doi:10.1093/nar/gkm649. PMC 2094063. PMID 17726044. 
  3. ^ Mackler S, Pacchioni A, Degnan R, Homan Y, Conti AC, Kalivas P, Blendy JA (February 2008). "Requirement for the POZ/BTB protein NAC1 in acute but not chronic psychomotor stimulant response". Behav. Brain Res. 187 (1): 48–55. doi:10.1016/j.bbr.2007.08.036. PMC 2248375. PMID 17945361. 
  4. ^ Krauss V, Dorn R (April 2004). "Evolution of the trans-splicing Drosophila locus mod(mdg4) in several species of Diptera and Lepidoptera". Gene 331: 165–76. doi:10.1016/j.gene.2004.02.019. PMID 15094203. 
  5. ^ Murcia-Nicolas A, Bolbach G, Blais JC, Beaud G (January 1999). "Identification by mass spectroscopy of three major early proteins associated with virosomes in vaccinia virus-infected cells". Virus Res. 59 (1): 1–12. doi:10.1016/S0168-1702(98)00114-2. PMID 10854161. 
  6. ^ a b Abhiman S, Iyer LM, Aravind L (February 2008). "BEN: a novel domain in chromatin factors and DNA viral proteins". Bioinformatics 24 (4): 458–61. doi:10.1093/bioinformatics/btn007. PMC 2477736. PMID 18203771. 

This article incorporates text from the public domain Pfam and InterPro IPR018379

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

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BEN domain Provide feedback

The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription [1].

Literature references

  1. Abhiman S, Iyer LM, Aravind L; , Bioinformatics. 2008;24:458-461.: BEN: a novel domain in chromatin factors and DNA viral proteins. PUBMED:18203771 EPMC:18203771


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018379

The BEN domain is found in diverse proteins including:

  • SMAR1 (Scaffold/Matrix attachment region-binding protein 1; also known as BANP), a tumour-suppressor MAR-binding protein that down-regulates Cyclin D1 expression by recruiting HDAC1-mSin3A co-repressor complex at Cyclin D1 promoter locus; SMAR1 is the target of prostaglandin A2 (PGA2) induced growth arrest [PUBMED:16166625, PUBMED:17726044].
  • NAC1, a novel member of the POZ/BTB (Pox virus and Zinc finger/Bric-a-bracTramtrack Broad complex), but which varies from other proteins of this class in that it lacks the characteristic DNA-binding motif [PUBMED:17945361].
  • Mod(mdg4) isoform C, the modifier of the mdg4 locus in Drosophila melanogaster (Fruit fly), where mdg4 encodes chromatin proteins which are involved in position effect variegation, establishment of chromatin boundaries, nerve path finding, meiotic chromosome pairing and apoptosis [PUBMED:15094203]. Trans-splicing of Mod(mdg4) produces at least 26 transcripts.
  • E5R protein from Chordopoxvirus virosomes, which is found in cytoplasmic sites of viral DNA replication [PUBMED:10854161].
  • Several proteins of polydnaviruses.

The BEN domain is predicted to function as an adaptor for the higher-order structuring of chromatin, and recruitment of chromatin modifying factors in transcriptional regulation. It has been suggested to mediate protein-DNA and protein-protein interactions during chromatin organisation and transcription. The presence of BEN domains in a poxviral early virosomal protein and in polydnaviral proteins also suggests a possible role in the organisation of viral DNA during replication or transcription. They are generally linked to other globular domains with functions related to transcriptional regulation and chromatin structure, such as BTB, C4DM, and C2H2 fingers [PUBMED:18203771].

This domain is predicted to form an all-alpha fold with four conserved helices. Its conservation pattern reveals several conserved residues, most of which have hydrophobic side-chains and are likely to stabilise the fold through helix-helix packing [PUBMED:18203771].

Domain organisation

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Alignments

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  Seed
(70)
Full
(842)
Representative proteomes NCBI
(780)
Meta
(0)
RP15
(71)
RP35
(102)
RP55
(212)
RP75
(412)
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  Seed
(70)
Full
(842)
Representative proteomes NCBI
(780)
Meta
(0)
RP15
(71)
RP35
(102)
RP55
(212)
RP75
(412)
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External links

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Curation and family details

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Seed source: Lakshminarayan I
Previous IDs: none
Type: Domain
Author: Lakshminarayan I, Bateman A
Number in seed: 70
Number in full: 842
Average length of the domain: 78.60 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 21.22 %

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 21.3 21.3
Trusted cut-off 21.4 21.6
Noise cut-off 21.2 21.1
Model length: 79
Family (HMM) version: 4
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