Summary: Ribbon-helix-helix protein, copG family
Ribbon-helix-helix protein, copG family Provide feedback
The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement . The helix-turn-helix-like structure is involved in dimerisation and not DNA binding as might have been expected .
Acebo P, Garcia de Lacoba M, Rivas G, Andreu JM, Espinosa M, del Solar G , Proteins 1998;32:248-261.: Structural features of the plasmid pMV158-encoded transcriptional repressor CopG, a protein sharing similarities with both helix-turn-helix and beta-sheet DNA binding proteins. PUBMED:9714164 EPMC:9714164
Gomis-R th FX, Sol M, Acebo P, Parraga A, Guasch A, Eritja R, Gonzalez A, Espinosa M, del Solar G, Coll M , EMBO J 1998;17:7404-7415.: The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator. PUBMED:9857196 EPMC:9857196
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002145
The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement [PUBMED:9857196]. The helix-turn-helix-like structure is involved in dimerisation and not DNA binding as might have been expected [PUBMED:9857196].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||regulation of transcription, DNA-templated (GO:0006355)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This superfamily contains many antitoxin families, all of which carry a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA .
The clan contains the following 26 members:Arc BrnA_antitoxin CcdA CopG_antitoxin DUF1778 DUF2610 HicB HicB-like_2 HicB_lk_antitox MetJ Omega_Repress ParD ParD_antitoxin ParD_like ParG PSK_trans_fac REGB_T4 RelB RepB-RCR_reg RHH_1 RHH_3 RHH_4 RHH_5 RHH_7 TraY VapB_antitoxin
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Bateman A|
|Number in seed:||32|
|Number in full:||33433|
|Average length of the domain:||38.30 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||41.89 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
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There are 4 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 RHH_1 domain has been found. There are 68 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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