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45  structures 4455  species 1  interaction 11816  sequences 10  architectures

Family: Bac_DNA_binding (PF00216)

Summary: Bacterial DNA-binding protein

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This is the Wikipedia entry entitled "Bacterial DNA binding protein". More...

Bacterial DNA binding protein Edit Wikipedia article

Bac_DNA_binding
PDB 1p51 EBI.jpg
anabaena hu-dna cocrystal structure (ahu6)
Identifiers
Symbol Bac_DNA_binding
Pfam PF00216
InterPro IPR000119
PROSITE PDOC00044
SCOP 1hue
SUPERFAMILY 1hue

In molecular biology, bacterial DNA binding proteins are a family of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins.[1][2] Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae.[3] The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [4] is found in enterobacteria and viral proteins include the African Swine Fever virus protein A104R (or LMW5-AR).[5]

The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins.[6] The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA.

References[edit]

  1. ^ Drlica K, Rouviere-Yaniv J (September 1987). "Histonelike proteins of bacteria". Microbiol. Rev. 51 (3): 301–19. PMC 373113. PMID 3118156. 
  2. ^ Pettijohn DE (September 1988). "Histone-like proteins and bacterial chromosome structure". J. Biol. Chem. 263 (26): 12793–6. PMID 3047111. 
  3. ^ Wang SL, Liu XQ (December 1991). "The plastid genome of Cryptomonas phi encodes an hsp70-like protein, a histone-like protein, and an acyl carrier protein". Proc. Natl. Acad. Sci. U.S.A. 88 (23): 10783–7. doi:10.1073/pnas.88.23.10783. PMC 53015. PMID 1961745. 
  4. ^ Friedman DI (November 1988). "Integration host factor: a protein for all reasons". Cell 55 (4): 545–54. doi:10.1016/0092-8674(88)90213-9. PMID 2972385. 
  5. ^ Neilan JG, Lu Z, Kutish GF, Sussman MD, Roberts PC, Yozawa T, Rock DL (March 1993). "An African swine fever virus gene with similarity to bacterial DNA binding proteins, bacterial integration host factors, and the Bacillus phage SPO1 transcription factor, TF1". Nucleic Acids Res. 21 (6): 1496. doi:10.1093/nar/21.6.1496. PMC 309344. PMID 8464748. 
  6. ^ Tanaka I, Appelt K, Dijk J, White SW, Wilson KS (1984). "3-A resolution structure of a protein with histone-like properties in prokaryotes". Nature 310 (5976): 376–81. doi:10.1038/310376a0. PMID 6540370. 

This article incorporates text from the public domain Pfam and InterPro IPR000119

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.

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Literature references

  1. Vis H, Mariani M, Vorgias CE, Wilson KS, Kaptein R, Boelens R; , J Mol Biol 1995;254:692-703.: Solution structure of the HU protein from Bacillus stearothermophilus. PUBMED:7500343 EPMC:7500343


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000119

Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [PUBMED:3118156, PUBMED:3047111]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae [PUBMED:1961745]. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [PUBMED:2972385] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) [PUBMED:8464748].

The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins [PUBMED:6540370]. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA.

Gene Ontology

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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 IHF-likeDNA-bdg (CL0548), which has the following description:

This superfamily is characterised by being a dimer of identical subunits of a core of four helices in a bundle, partly opened, capped with a beta-sheet. All members appear to be prokaryotic DNA-binding domains.

The clan contains the following 3 members:

Bac_DNA_binding HU-DNA_bdg Tra_M

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(158)
Full
(11816)
Representative proteomes NCBI
(6533)
Meta
(4975)
RP15
(797)
RP35
(1619)
RP55
(2112)
RP75
(2522)
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Format an alignment

  Seed
(158)
Full
(11816)
Representative proteomes NCBI
(6533)
Meta
(4975)
RP15
(797)
RP35
(1619)
RP55
(2112)
RP75
(2522)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(158)
Full
(11816)
Representative proteomes NCBI
(6533)
Meta
(4975)
RP15
(797)
RP35
(1619)
RP55
(2112)
RP75
(2522)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

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.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

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.

Note: You can also download the data file for the tree.

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: Prosite
Previous IDs: none
Type: Domain
Author: Finn RD
Number in seed: 158
Number in full: 11816
Average length of the domain: 89.30 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 83.62 %

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 20.9 20.9
Trusted cut-off 20.9 20.9
Noise cut-off 20.8 20.8
Model length: 90
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Bac_DNA_binding

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 Bac_DNA_binding domain has been found. There are 45 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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