Protein Family Models

This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. [1]. 18361456. Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source. Li Y, Bahti P, Shaw N, Song G, Chen S, Zhang X, Zhang M, Cheng C, Yin J, Zhu JY, Zhang H, Che D, Xu H, Abbas A, Wang BC, Liu ZJ;. Proteins 2008;71:2109-13. (from Pfam)

Date:

2024-10-16

This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins [1]. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity [1]. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division [2]. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases [4]. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks. [1]. 9722641. Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Aravind L, Leipe DD, Koonin EV;. Nucleic Acids Res 1998;26:4205-4213. [2]. 9224947. Cloning and analysis of the dnaG gene encoding Pseudomonas putida DNA primase. Szafranski P, Smith CL, Cantor CR;. Biochim Biophys Acta 1997;1352:243-248. [3]. 8294018. The Haemophilus influenzae dnaG sequence and conserved bacterial primase motifs. Versalovic J, Lupski JR;. Gene 1993;136:281-286. [4]. 9121560. An atypical topoisomerase II from Archaea with implications for meiotic recombination. Bergerat A, de Massy B, Gadelle D, Varoutas PC, Nicolas A, Forterre P;. Nature 1997;386:414-417. (from Pfam)

Date:

2024-10-16

This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119. [1]. 1646964. Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Wigley DB, Davies GJ, Dodson EJ, Maxwell A, Dodson G;. Nature 1991;351:624-629. [2]. 10734094. Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center. Brino L, Urzhumtsev A, Mousli M, Bronner C, Mitschler A, Oudet P, Moras D. J Biol Chem 2000;275:9468-9475. [3]. 10575351. Isoleucine 10 is essential for DNA gyrase B function in Escherichia coli. Brino L, Bronner C, Oudet P, Mousli M. Biochimie 1999;81:973-980. [4]. 9817206. NMR structure of the histidine kinase domain of the E. coli osmosensor EnvZ. Tanaka T, Saha SK, Tomomori C, Ishima R, Liu D, Tong KI, Park H, Dutta R, Qin L, Swindells MB, Yamazaki T, Ono AM, Kainosho M, Inouye M, Ikura M. Nature 1998;396:88-92. [5]. 9657678. Identification of a residue involved in transition-state stabilization in the ATPase reaction of DNA gyrase. Smith CV, Maxwell A. Biochemistry 1998;37:9658-9667. [6]. 9230303. Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone. Prodromou C, Roe SM, O'Brien R, Ladbury JE, Piper PW, Pearl LH. Cell 1997;90:65-75. (from Pfam)

Date:

2024-10-16

The amino terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different carboxyl terminus. The amino-terminal portion of the DNA gyrase B protein is thought to catalyse the ATP-dependent super-coiling of DNA. See Pfam:PF00204. The carboxyl-terminal end supports the complexation with the DNA gyrase A protein and the ATP-independent relaxation. This family also contains Topoisomerase IV. This is a bacterial enzyme that is closely related to DNA gyrase, [1]. [1]. 7770916. The mechanisms of DNA topoisomerases. Roca J;. Trends Biochem Sci 1995;20:156-160. (from Pfam)

Date:

2024-10-16

DNA topoisomerase subunit B relaxes positive DNA supercoils generated during DNA replication; such as Staphylococcus aureus DNA topoisomerase IV subunit B and Bacillus subtilis DNA gyrase subunit B

Date:

2022-08-18

Negatively supercoils closed circular double-stranded DNA

Date:

2020-10-26

Negatively supercoils closed circular double-stranded DNA

Date:

2022-01-26

This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB.

Gene:

gyrB

Date:

2024-05-15