G3p: Difference between revisions
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==Overview== | ==Overview== | ||
Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. | '''Gene 3 protein''' (g3p pr pIII) is a '''minor coat protein''' found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. | ||
==Structural Analysis== | ==Structural Analysis== | ||
<applet load='1g3p' size=' | <applet load='1g3p' size='350' frame='true' align='right' caption='D1 and D2 domains of g3p complex with sulfate [[1g3p]]' /> | ||
Five major papers will be discussed outlining the evolution of structure analysis of g3p. | Five major papers will be discussed outlining the evolution of structure analysis of g3p. | ||
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One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. | One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. | ||
Finally, two papers <ref name="lubkowski 99"> PMID: 10404600 </ref> <ref name="deprez"> PMID:15701516 </ref> were later published described interactions between g3p and TolA protein (located on the host cell, see [[Infectivity]]. | Finally, two papers <ref name="lubkowski 99"> PMID: 10404600 </ref> <ref name="deprez"> PMID:15701516 </ref> were later published described interactions between g3p and TolA protein (located on the host cell, see [[#Infectivity]]. | ||
===D1 Domain=== | ===D1 Domain=== | ||
<applet load=' | <applet load='2g3p' size='350' frame='true' align='left' caption='[[2g3p]] Representation is a dimer of two molecules of D1 and D2 domains of g3p' /> | ||
The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>. | The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>. | ||
The <scene name='G3p/D1_in_blue_spin/1'>D1 domain</scene> consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. | The <scene name='G3p/D1_in_blue_spin/1'>D1 domain</scene> consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. | ||
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==Functional Implications== | ==Functional Implications== | ||
===Infectivity=== | ===Infectivity=== | ||
<applet load='1tol' size='350' frame='true' align='right' caption='D1 of g3p interacting with D3 of TolA [[1tol]]' /> | |||
The function of the protein has a close correlation with its structural domains. The D1 domain interacts with TolA protein in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. | The function of the protein has a close correlation with its structural domains. The <scene name='G3p/D1_and_tola/1'>D1 domain (blue) interacts with TolA protein (orange)</scene> in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. | ||
The function of D3 was elicited last. D3 domain “anchors” to F pilus and is necessary for phage packaging<ref name="holliger 99"/>. | The function of D3 was elicited last. D3 domain “anchors” to F pilus and is necessary for phage packaging<ref name="holliger 99"/>. | ||
===Phage Display=== | ===Phage Display=== | ||
Infection with filamentous phage does not cause host cell lysis or death | Infection with filamentous phage does not cause host cell lysis or death <ref name="gailus"> PMID:8026502 </ref>. The N terminus of g3p can be truncated and the peptide of choice can be inserted <ref name="cabilly"/>. Insertions can also be made between D2 and D3 <ref name="h and r"> PMID: 9032075 </ref>. Specifically, fusions to ther N terminus have no affect on infectivity, between D12 and D3 have 100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides <ref name="chatellier"/>. | ||
N terminus can be truncated and the peptide of choice can be inserted | |||
Insertions can also be | |||
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"/>. | 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"/>. | ||
While the N terminus domain is necessary for infection, the full protein does not need to exist for all five particles on the surface <ref name="cabilly"/>. | |||
==Evolutionarily Related Proteins== | ==Evolutionarily Related Proteins== | ||
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Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075) | Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075) | ||
==3D structures of G3p== | |||
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} | |||
[[ | [[2x9b]] – IF1G3p TolA-binding domain – Enterobacteria phage IF1<br /> | ||
[[ | [[2x9a]] – IF1G3p TolA-binding domain + TolA C-terminal domain<br /> | ||
[[ | [[3knq]], [[2g3p]] - FDG3p N-terminal – Enterobacteria phage FD<br /> | ||
[[ | [[3dgs]] - FDG3p N-terminal (mutant)<br /> | ||
[[ | [[1fgp]] – FDG3p membrane penetration domain 20-85 - NMR<br /> | ||
[[9g8e]] – FDG3p N2 domain 120-223 - NMR<br /> | |||
[[8b3o]] – F1G3p + G8p + G6p – Enterobacteria phage F1 – Cryo EM<br /> | |||
[[8ixk]], [[8jwx]] – M13G3p + G8p + G6p – Inovirus M13 – Cryo EM<br /> | |||
[[1tol]] – M13G3p N-terminal domain/ M13TolA C-terminal domain – Enterobacteria phage M13<br /> | |||
[[1g3p]] - M13G3p N-terminal domain<br /> | |||
[[4eo0]], [[4eo1]] - IKEG3p pilus-binding domain – Enterobacteria phage IKE | |||
==References== | ==References== | ||
<references/> | <references/> | ||
[[Category:Topic Page]] | |||
