Protein Family Models

This entry represents the DNAse domain from colicin/pyocin bacteriocins, such as pyocin-S2 from Pseudomonas aeruginosa and colicin E7/E9 from E. coli. This domain has an alpha/beta fold containing a Zn2+ ion binding site [1-5]. Paper describing PDB structure 1m08. [1]. 12441102. The crystal structure of the nuclease domain of colicin E7 suggests a mechanism for binding to double-stranded DNA by the H-N-H endonucleases. Cheng YS, Hsia KC, Doudeva LG, Chak KF, Yuan HS;. J Mol Biol. 2002;324:227-236. Paper describing PDB structure 1mz8. [2]. 12441392. Metal ions and phosphate binding in the H-N-H motif: crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions. Sui MJ, Tsai LC, Hsia KC, Doudeva LG, Ku WY, Han GW, Yuan HS;. Protein Sci. 2002;11:2947-2957. Paper describing PDB structure 1pt3. [3]. 14962381. DNA binding and degradation by the HNH protein ColE7. Hsia KC, Chak KF, Liang PH, Cheng YS, Ku WY, Yuan HS;. Structure. 2004;12:205-214. Paper describing PDB structure 1ujz. [4]. 15034550. Computational redesign of protein-protein interaction specificity. Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D;. Nat Struct Mol Biol. 2004;11:371-379. Paper describing PDB structure 1v13. [5]. 15190054. Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases. Mate MJ, Kleanthous C;. J Biol Chem. 2004;279:34763-34769. (from Pfam)

Date:

2024-10-16

This family represents a conserved region approximately 180 residues long within bacterial S-type pyocins. Pyocins are polypeptide toxins produced by, and active against, bacteria. S-type pyocins cause cell death by DNA breakdown due to endonuclease activity [1]. [1]. 12423794. The pyocins of Pseudomonas aeruginosa. Michel-Briand Y, Baysse C;. Biochimie 2002;84:499-510. (from Pfam)

Date:

2024-10-16

HCP is a family of proteins which are expressed in up to 1000 copies in Gram-negative bacteria. Together these copies aggregate into a needle-like shaft or tube that will penetrate other bacteria via a puncturing protein attached to its head [1]. Initially Hcp forms a hexameric structure with a central channel of 40 Angstroms. These hexamers pile up one on top of each other forming nanotubes resembling the gp19 tail phage tube [2]. [1]. 24381728. The rise of the Type VI secretion system. Filloux A;. F1000Prime Rep. 2013;5:52. [2]. 16763151. A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus. Mougous JD, Cuff ME, Raunser S, Shen A, Zhou M, Gifford CA, Goodman AL, Joachimiak G, Ordonez CL, Lory S, Walz T, Joachimiak A, Mekalanos JJ;. Science. 2006;312:1526-1530. (from Pfam)

Date:

2024-10-16

HNH endonuclease signature motif containing protein catalyzes the hydrolysis of DNA

Date:

2017-03-02

TssD, originally called Hcp1 (hemolysin coregulated protein), forms hexameric ring-shaped structures that stack to form the tube of type VI secretion systems (T6SS).(PMID:17660433). Pathogens may have many multiple members of this family, with three to ten in Erwinia carotovora, Yersinia pestis, uropathogenic Escherichia coli, and the insect pathogen Photorhabdus luminescens.

Gene:

tssD

Date:

2024-08-07