G3p: Difference between revisions
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===Structural Analysis=== | ===Structural Analysis=== | ||
Lubkowski et al<ref name="lubkowski"/> crystallized N1 and N2 together using | |||
His tag | His tag | ||
Redox shuffle to form disulfide bonds | Redox shuffle to form disulfide bonds | ||
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Important characteristics: | Important characteristics: | ||
Cis proline near c terminal end | Cis proline near c terminal end <ref name="lubkowski"/> | ||
Oxidation of tryptophan | Oxidation of tryptophan <ref name="lubkowski"/> not found in other structures (Holliger et al) | ||
N1 domain | |||
Initial alpha helix at N terminal domain | ====N1 domain==== | ||
Five beta strands arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet | Initial alpha helix at N terminal domain <ref name="lubkowski"/> | ||
Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) | Five beta strands arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/> | ||
N2 domain | Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/> | ||
- 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet | |||
Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions | ====N2 domain==== | ||
3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) | - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/> | ||
One alpha helix that interacts with rest of N2 domain by hydrophobic interactions | Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/> | ||
3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/> | |||
One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/> | |||
Cation pi interaction between His 191 and Phe 199 | Cation pi interaction between His 191 and Phe 199 | ||
C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation | C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation | ||
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===Functional Implications=== | ===Functional Implications=== | ||
====Infectivity==== | ====Infectivity==== | ||
The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity | The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. | ||
N1 interacts with TolA protein anchoring it to bacterial cell. ( | N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly) see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997) | ||
N1 and N2 have 15% identity | N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication | ||
D2 domain binds to F pilus (Chatellier et al) | D2 domain binds to F pilus (Chatellier et al) | ||
D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al) | D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al) | ||
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Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al). | Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al). | ||
The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). | The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). | ||
Horseshoe shaped molecule with polar molecules facing toward the center | Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? | ||
Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe | Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>. | ||
Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly). | Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly). | ||
Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al) | Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al) | ||
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===Evolutionarily Related Proteins=== | ===Evolutionarily Related Proteins=== | ||
N1 and N2 have 15% identity | N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication | ||
Used DALI to identify similar proteins with both domains | Used DALI to identify similar proteins with both domains <ref name="lubkowski"/> did not identify any | ||
When looking at each domain, they found some similar proteins | When looking at each domain, they found some similar proteins | ||
N2 | ====N2==== | ||
PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 | PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075) | ||
PTB domain H and R, 9032075) | PTB domain H and R, 9032075) | ||
N1 | ====N1==== | ||
Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) | Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/> | ||
Compared with permuted SH3 domain (1tuc), but no sequence homology | Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/> | ||
===Links to Available Structures=== | ===Links to Available Structures=== | ||
===References=== | ===References=== | ||
<references/> | <references/> | ||
