Summary: GyrI-like small molecule binding domain
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GyrI-like small molecule binding domain Provide feedback
This family contains the small molecule binding domain of a number of different bacterial transcription activators . This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding . The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira .
Romanowski MJ, Gibney SA, Burley SK; , Proteins 2002;47:403-407.: Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17. PUBMED:11948793 EPMC:11948793
Anantharaman V, Aravind L;, Proteins. 2004;56:795-807.: The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. PUBMED:15281131 EPMC:15281131
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR010499
This domain is found in the probable effector binding domain of a number of different bacterial transcription activators [PUBMED:10802742] and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.
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SHS2 is a novel domain with a simple fold containing a core of 3 strands, forming a curved sheet, and a single helix in a strand-helix-strand-strand (SHS2) configuration . SHS2 is found in the bacterial cell division ATPase FtsA, the archaeo-eukaryotic RNA polymerase subunit Rpb7p, the GyrI superfamily, and the uncharacterized MTH1598/Tm1083-like proteins . The fold exists as single copy versions in FtsA (where it is inserted into the RNAseH fold), Rbp7p and Dodecin . It is found as a diad in the GyrI superfamily. In MTH1598/Tm1083-like proteins two copies of SHS2 are found with one inserted into another . The single-copy versions in FtsA and Rbp7 mediate proteinprotein interactions, while the one in Dodecin is a small molecule binding domain. The GyrI also binds small molecule, while the MTH1598 is predicted to be enzymatic .
The clan contains the following 7 members:Archease Cass2 Dodecin GyrI-like SHS2_FTSA SHS2_Rpb7-N SOUL
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Curation and family details
|Seed source:||Pfam-B_36124 (release 9.0)|
|Author:||Finn RD, Anantharaman V|
|Number in seed:||88|
|Number in full:||6066|
|Average length of the domain:||155.40 aa|
|Average identity of full alignment:||16 %|
|Average coverage of the sequence by the domain:||64.70 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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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 GyrI-like domain has been found. There are 26 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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