Protein Family Models

This domain, approximately 150 residues, is mainly found in several uncharacterized proteins in various Prochlorococcus and Synechococcus species. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity [1]. The specific function of this family is unknown, but the structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing [1]. [1]. 19173316. Crystal structure of a novel Sm-like protein of putative. cyanophage origin at 2.60 A resolution.. Das D, Kozbial P, Axelrod HL, Miller MD, McMullan D, Krishna SS,. Abdubek P, Acosta C, Astakhova T, Burra P, Carlton D, Chen C,. Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA,. Ernst D, Farr C, Feuerhelm J, Grzechnik A, Grzechnik SK, Hale J,. Han GW, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW,. Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E,. Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R,. Rife CL, Sefcovic N, Sudek S, Tien H, Trame C, Trout CV, van den. Be, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM,. Godzik A, Lesley SA and Wilson IA.. Proteins 75 (2), 296-307 (2009) (from Pfam)

Date:

2024-08-14

The structure of one member of the ABATE domain family consists of a two-domain organisation, with the N-terminal domain presenting a new fold called the ABATE domain that may bind an as yet unknown ligand. The C-terminal domain forms a treble-clef zinc-finger that is likely to be involved in DNA binding. suggests a role as stress-induced transcriptional regulator. Further computational analyses sugeests a role as a stress-induced transcriptional regulator [1]. Members of this family are found in Streptomyces, Rhizobium, Ralstonia, Agrobacterium and Bradyrhizobium species. [1]. 20944211. The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45. A resolution reveals a new fold (the ABATE domain) and suggests. its possible role as a transcription regulator.. Bakolitsa C, Bateman A, Jin KK, McMullan D, Krishna SS, Miller. MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P,. Carlton D, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elias. Y, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW,. Jaroszewski L, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano. D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S,. Paulsen J, Reyes R, Rife CL, Sefcovic N, Tien H, Trame CB, Trout. CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley. J, Elsliger MA, Deacon AM, Godzik A, Lesley S, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1198-1204. (from Pfam)

Date:

2024-08-14

This family of proteins is structurally similar to proteins with the Bacillus chorismate mutase-like (BCM-like) fold. This structure, combined with its genomic context, suggest that it has a role in amino acid synthesis [1]. [1]. 20944209. Structures of the first representatives of Pfam family PF06684. (DUF1185) reveal a novel variant of the Bacillus chorismate. mutase fold and suggest a role in amino-acid metabolism.. Bakolitsa C, Kumar A, Jin KK, McMullan D, Krishna SS, Miller MD,. Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton. D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elias. Y, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik. A, Grzechnik SK, Han GW, Jaroszewski L, Johnson HA, Klock HE,. Knuth MW, Kozbial P, Marciano D, Morse AT, Murphy KD,. Nigoghossian E, Nopakun A, Okach L, Paulsen J, Puckett C, Reyes. R, Rife CL, Sefcovic N, Tien HJ, Trame CB, Trout CV, van den. Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger. MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1182-1189. (from Pfam)

Date:

2024-08-14

PDDEXK_6 is a family of plant proteins that are distant homologues of the PD-(D/E)XK nuclease superfamily. The core structure is retained, as alpha-beta-beta-beta-alpha-beta. It retains the characteristic PDDEXK motifs II and III in modified forms - xDxxx motif located in the second core beta-strand, where x is any hydrophobic residue, and a D/E)X(D/N/S/C/G) pattern. The missing positively charged residue in motif III is possibly replaced by a conserved arginine in motif IV located in the proceeding alpha-helix [1]. The family is not in general fused with any other domains, so its function cannot be predicted [2]. [1]. 17584917. Realm of PD-(D/E)XK nuclease superfamily revisited: detection of. novel families with modified transitive meta profile searches.. Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K;. BMC Struct Biol. 2007;7:40.. [2]. 22936940. Conserved Peptide Upstream Open Reading Frames are Associated. with Regulatory Genes in Angiosperms.. Jorgensen RA, Dorantes-Acosta AE;. Front Plant Sci. 2012;3:191. (from Pfam)

Date:

2024-08-14

EspB is a type-III-secreted pore-forming protein of enteropathogenic Escherichia coli (EPEC) which is essential for EPEC pathogenesis [1]. EspB is also found in Citrobacter rodentium [2]. [1]. 12071694. Expression and purification of the recombinant enteropathogenic. Escherichia coli vaccine candidates BfpA and EspB.. Quintana Flores VM, Campos de Souza Fernandes RC, Sousa de. Macedo Z, Medina-Acosta E;. Protein Expr Purif 2002;25:16-22.. [2]. 12405637. Comparison of an espB gene fecal polymerase chain reaction assay. with bacteriologic isolation for detection of Citrobacter. rodentium infection in mice.. McKeel R, Douris N, Foley PL, Feldman SH;. Comp Med 2002;52:439-444. (from Pfam)

Date:

2024-08-14