Journal: BMC Bioinformatics

Article Title: Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions

doi: 10.1186/s12859-014-0434-7

Figure Lengend Snippet: Structures of the N-terminally truncated Bacteroides proteins BVU_4064 and BF1687 (PDB codes 3kog and 3g3l, respectively). The N-terminal domain (in slate blue color) and the C-terminal domain (in orange color) of the 3kog structure show significant similarities with the corresponding domains of 3g3l structure (N and C terminal domains shown in pale cyan and wheat colors respectively). In contrast, the region connecting the domains (in green) is clearly different in the two structures: a short linker in 3kog, an extended 4-helix insertion and one extra strand that is added to the C-terminal domain in 3g3l. A histidine-rich region present at the C-terminus in both of our proteins is found ordered only in the 3kog structure (see box with text in the Figure).

Article Snippet: The crystal structures of the N-terminally truncated Bacteroides proteins BVU_4064 ( Bacteroides vulgatus strain ATCC 8482, JCSG target ID: 393242, GenBank accession: YP_001301288.1, PDB code: 3kog) and BF1687 ( Bacteroides fragilis strain NCTC 9343, JCSG target ID: 393243, Gene Bank accession: YP_211325.1, PDB code: 3g3l) have been determined to 1.85 Å and 2.2 Å resolution, using MAD and SAD phasing methods respectively as described in the section.

Techniques:

Journal: BMC Bioinformatics

Article Title: Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions

doi: 10.1186/s12859-014-0434-7

Figure Lengend Snippet: Superposition of 3kog and 3g3l structures. (A) Corresponding domains (colored in slate blue and pale cyan for N-terminal domains; orange and wheat for C-terminal domains; linker region in green) in the two structures superimpose fairly well with an overall RMSD of 3.7 Å for the 166 equivalent positions in the rigid-body alignment . (B) Stereo view of N and C terminal domains shown separately with linker regions removed to highlight the structural similarity.

Article Snippet: The crystal structures of the N-terminally truncated Bacteroides proteins BVU_4064 ( Bacteroides vulgatus strain ATCC 8482, JCSG target ID: 393242, GenBank accession: YP_001301288.1, PDB code: 3kog) and BF1687 ( Bacteroides fragilis strain NCTC 9343, JCSG target ID: 393243, Gene Bank accession: YP_211325.1, PDB code: 3g3l) have been determined to 1.85 Å and 2.2 Å resolution, using MAD and SAD phasing methods respectively as described in the section.

Techniques:

Journal: BMC Bioinformatics

Article Title: Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions

doi: 10.1186/s12859-014-0434-7

Figure Lengend Snippet: Structural similarities of the N-terminal domains. (A-F) Pre-albumin-like fold of the N-terminal domains in 3kog and 3g3l structures that is also present as a cell adhesion modules in several proteins belonging to the Transthyretin superfamily. (G) Alignment between the lipoprotein signal sequences present at the N-terminus of BVU_4064 and BF1687. The arrow points to the conserved CYS residue in the consensus sequence for the protein family PF12985.

Article Snippet: The crystal structures of the N-terminally truncated Bacteroides proteins BVU_4064 ( Bacteroides vulgatus strain ATCC 8482, JCSG target ID: 393242, GenBank accession: YP_001301288.1, PDB code: 3kog) and BF1687 ( Bacteroides fragilis strain NCTC 9343, JCSG target ID: 393243, Gene Bank accession: YP_211325.1, PDB code: 3g3l) have been determined to 1.85 Å and 2.2 Å resolution, using MAD and SAD phasing methods respectively as described in the section.

Techniques: Residue, Sequencing

Journal: BMC Bioinformatics

Article Title: Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions

doi: 10.1186/s12859-014-0434-7

Figure Lengend Snippet: Structural similarities of the C-terminal domain of 3kog and 3g3l with bacterial pore-forming toxins. The region shown in red is implicated in membrane insertion in the pore-forming toxins [epsilon toxin (PDB code: 1uyj) and aerolysin (PDB code: 1z52)] and in the hemolytic lectin (PDB code 1w3g). In both 3kog and 3g3l this region corresponds to a helical insertion.

Article Snippet: The crystal structures of the N-terminally truncated Bacteroides proteins BVU_4064 ( Bacteroides vulgatus strain ATCC 8482, JCSG target ID: 393242, GenBank accession: YP_001301288.1, PDB code: 3kog) and BF1687 ( Bacteroides fragilis strain NCTC 9343, JCSG target ID: 393243, Gene Bank accession: YP_211325.1, PDB code: 3g3l) have been determined to 1.85 Å and 2.2 Å resolution, using MAD and SAD phasing methods respectively as described in the section.

Techniques: Membrane