Colicin E9 - Revision history

Gemma McGoldrick: /* Mechanism of uptake */

Gemma McGoldrick — Sun, 27 Mar 2011 17:20:28 GMT

Mechanism of uptake

←Older revision		Revision as of 17:20, 27 March 2011
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	The formation of a disulphide bond at D20C/E66C abolishes its channel forming ability, and its cytotoxicity (as it cannot penetrate cells) but has no effect on its DNase activity. It is still able to bind to the phospholipids, but not translocate across the membrane<ref> PMID: 15044477 </ref>.		The formation of a disulphide bond at D20C/E66C abolishes its channel forming ability, and its cytotoxicity (as it cannot penetrate cells) but has no effect on its DNase activity. It is still able to bind to the phospholipids, but not translocate across the membrane<ref> PMID: 15044477 </ref>.
		+
		+	This uptake is highly similar to the uptake of [[Colicin E3]].

	==Killing Activities==		==Killing Activities==

Gemma McGoldrick: /* Killing Activities */

Gemma McGoldrick — Sat, 26 Feb 2011 15:39:55 GMT

Killing Activities

←Older revision		Revision as of 15:39, 26 February 2011
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	==Killing Activities==		==Killing Activities==
-	{{STRUCTURE_1fsj \| PDB=1fsj \| SCENE= }}	+	{{STRUCTURE_1fsj \| PDB=1fsj \| SCENE= Colicin_E9/E9c/1 }}

	The cytotoxic activity of colE9 is DNase activity in the 15kDa C terminal domain, where it hydrolyses the DNA<ref> PMID: 12804762 </ref> <ref> PMID: 15452437 </ref>. However, it is also able to form ion channels in planar lipid bilayers, similar to the pore-forming colicins. These channels do not cause cell death, instead they are related to the ability of the E9 DNase domain to translocate across the inner membrane. The structure shows the crystal structure of the DNase domain.		The cytotoxic activity of colE9 is DNase activity in the 15kDa C terminal domain, where it hydrolyses the DNA<ref> PMID: 12804762 </ref> <ref> PMID: 15452437 </ref>. However, it is also able to form ion channels in planar lipid bilayers, similar to the pore-forming colicins. These channels do not cause cell death, instead they are related to the ability of the E9 DNase domain to translocate across the inner membrane. The structure shows the crystal structure of the DNase domain.

Gemma McGoldrick: /* Mechanism of uptake */

Gemma McGoldrick — Sat, 26 Feb 2011 15:36:46 GMT

Mechanism of uptake

←Older revision		Revision as of 15:36, 26 February 2011
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	{{STRUCTURE_2ivz \| PDB=2ivz \| SCENE= Colicin_E9/Monomercole9tolb/1 }}		{{STRUCTURE_2ivz \| PDB=2ivz \| SCENE= Colicin_E9/Monomercole9tolb/1 }}

-	The primary receptor for colicin E9 is the vitamin B12 receptor, BtuB. It then requires the outer membrane porin OmpF - either the two form the functional receptor, or OmpF is recruited for subsequent translocation. The OmpF association with the BtuB-colicin complex is weak and transient. After the interaction with OmpF, colicin E9 requires the [[TolB]] system to pass across the periplasm<ref> PMID: 12804762 </ref>. The interaction with TolB is governed by a pentapeptide region in the N terminus called the <scene name='Colicin_E9/Monomercole9t/1'>TolB box</scene>, where ColE9 folds into a distorted hairpin within the six-bladed β-propeller of TolB<ref> PMID: 16894158 </ref>. The residues surrounding these (from 34 to 46) are unstructured and highly flexible, but the TolB box of 5 residues (DGSGW) is organised within this disordered domain<ref> PMID: 15452437 </ref>. Within this pentapeptide sequence, the 3 essential resides are D35, S37 and W39. Mutations in all but one of these residues leads to a reduced affinity of binding to TolB<ref> PMID: 16166536 </ref>. Some regions in the entire site have reduced mobility relative to other regions, that form local hydrophobic clusters<ref> PMID: 15452437 </ref>.	+	The primary receptor for colicin E9 is the vitamin B12 receptor, BtuB. It then requires the outer membrane porin OmpF - either the two form the functional receptor, or OmpF is recruited for subsequent translocation. The OmpF association with the BtuB-colicin complex is weak and transient. After the interaction with OmpF, colicin E9 requires the [[TolB]] system to pass across the periplasm<ref> PMID: 12804762 </ref>. The interaction with <scene name='Colicin_E9/Monomertolb/1'>TolB</scene> is governed by a pentapeptide region in the N terminus called the <scene name='Colicin_E9/Monomercole9t/1'>TolB box</scene>, where ColE9 folds into a distorted hairpin within the six-bladed β-propeller of TolB<ref> PMID: 16894158 </ref>. The residues surrounding these (from 34 to 46) are unstructured and highly flexible, but the TolB box of 5 residues (DGSGW) is organised within this disordered domain<ref> PMID: 15452437 </ref>. Within this pentapeptide sequence, the 3 essential resides are D35, S37 and W39. Mutations in all but one of these residues leads to a reduced affinity of binding to TolB<ref> PMID: 16166536 </ref>. Some regions in the entire site have reduced mobility relative to other regions, that form local hydrophobic clusters<ref> PMID: 15452437 </ref>.

	OmpF acts synergistically with BtuB to protect bacteria against the action of colicin E9. This could indicate that OmpF is a component of the receptor apparatus. Alternatively the role of OmpF could be more to do with translocation rather than receptor recognition		OmpF acts synergistically with BtuB to protect bacteria against the action of colicin E9. This could indicate that OmpF is a component of the receptor apparatus. Alternatively the role of OmpF could be more to do with translocation rather than receptor recognition

Gemma McGoldrick: /* Mechanism of uptake */

Gemma McGoldrick — Sat, 26 Feb 2011 15:34:25 GMT

Mechanism of uptake

←Older revision		Revision as of 15:34, 26 February 2011
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	{{STRUCTURE_2ivz \| PDB=2ivz \| SCENE= Colicin_E9/Monomercole9tolb/1 }}		{{STRUCTURE_2ivz \| PDB=2ivz \| SCENE= Colicin_E9/Monomercole9tolb/1 }}

-	The primary receptor for colicin E9 is the vitamin B12 receptor, BtuB. It then requires the outer membrane porin OmpF - either the two form the functional receptor, or OmpF is recruited for subsequent translocation. The OmpF association with the BtuB-colicin complex is weak and transient. After the interaction with OmpF, colicin E9 requires the [[~~Tol~~]] system to pass across the periplasm<ref> PMID: 12804762 </ref>. The interaction with [[TolB]] is governed by a pentapeptide region in the N terminus called the TolB box, where ColE9 folds into a distorted hairpin within the six-bladed β-propeller of TolB<ref> PMID: 16894158 </ref>. The residues surrounding these (from 34 to 46) are unstructured and highly flexible, but the TolB box of 5 residues (DGSGW) is organised within this disordered domain<ref> PMID: 15452437 </ref>. Within this pentapeptide sequence, the 3 essential resides are D35, S37 and W39. Mutations in all but one of these residues leads to a reduced affinity of binding to TolB<ref> PMID: 16166536 </ref>. Some regions in the entire site have reduced mobility relative to other regions, that form local hydrophobic clusters<ref> PMID: 15452437 </ref>.	+	The primary receptor for colicin E9 is the vitamin B12 receptor, BtuB. It then requires the outer membrane porin OmpF - either the two form the functional receptor, or OmpF is recruited for subsequent translocation. The OmpF association with the BtuB-colicin complex is weak and transient. After the interaction with OmpF, colicin E9 requires the [[TolB]] system to pass across the periplasm<ref> PMID: 12804762 </ref>. The interaction with TolB is governed by a pentapeptide region in the N terminus called the <scene name='Colicin_E9/Monomercole9t/1'>TolB box</scene>, where ColE9 folds into a distorted hairpin within the six-bladed β-propeller of TolB<ref> PMID: 16894158 </ref>. The residues surrounding these (from 34 to 46) are unstructured and highly flexible, but the TolB box of 5 residues (DGSGW) is organised within this disordered domain<ref> PMID: 15452437 </ref>. Within this pentapeptide sequence, the 3 essential resides are D35, S37 and W39. Mutations in all but one of these residues leads to a reduced affinity of binding to TolB<ref> PMID: 16166536 </ref>. Some regions in the entire site have reduced mobility relative to other regions, that form local hydrophobic clusters<ref> PMID: 15452437 </ref>.

	OmpF acts synergistically with BtuB to protect bacteria against the action of colicin E9. This could indicate that OmpF is a component of the receptor apparatus. Alternatively the role of OmpF could be more to do with translocation rather than receptor recognition		OmpF acts synergistically with BtuB to protect bacteria against the action of colicin E9. This could indicate that OmpF is a component of the receptor apparatus. Alternatively the role of OmpF could be more to do with translocation rather than receptor recognition

Gemma McGoldrick: /* Mechanism of uptake */

Gemma McGoldrick — Sat, 26 Feb 2011 15:25:57 GMT

Mechanism of uptake

←Older revision		Revision as of 15:25, 26 February 2011
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	==Mechanism of uptake==		==Mechanism of uptake==
-	{{STRUCTURE_2ivz \| PDB=2ivz \| SCENE= }}	+	{{STRUCTURE_2ivz \| PDB=2ivz \| SCENE= Colicin_E9/Monomercole9tolb/1 }}

	The primary receptor for colicin E9 is the vitamin B12 receptor, BtuB. It then requires the outer membrane porin OmpF - either the two form the functional receptor, or OmpF is recruited for subsequent translocation. The OmpF association with the BtuB-colicin complex is weak and transient. After the interaction with OmpF, colicin E9 requires the [[Tol]] system to pass across the periplasm<ref> PMID: 12804762 </ref>. The interaction with [[TolB]] is governed by a pentapeptide region in the N terminus called the TolB box, where ColE9 folds into a distorted hairpin within the six-bladed β-propeller of TolB<ref> PMID: 16894158 </ref>. The residues surrounding these (from 34 to 46) are unstructured and highly flexible, but the TolB box of 5 residues (DGSGW) is organised within this disordered domain<ref> PMID: 15452437 </ref>. Within this pentapeptide sequence, the 3 essential resides are D35, S37 and W39. Mutations in all but one of these residues leads to a reduced affinity of binding to TolB<ref> PMID: 16166536 </ref>. Some regions in the entire site have reduced mobility relative to other regions, that form local hydrophobic clusters<ref> PMID: 15452437 </ref>.		The primary receptor for colicin E9 is the vitamin B12 receptor, BtuB. It then requires the outer membrane porin OmpF - either the two form the functional receptor, or OmpF is recruited for subsequent translocation. The OmpF association with the BtuB-colicin complex is weak and transient. After the interaction with OmpF, colicin E9 requires the [[Tol]] system to pass across the periplasm<ref> PMID: 12804762 </ref>. The interaction with [[TolB]] is governed by a pentapeptide region in the N terminus called the TolB box, where ColE9 folds into a distorted hairpin within the six-bladed β-propeller of TolB<ref> PMID: 16894158 </ref>. The residues surrounding these (from 34 to 46) are unstructured and highly flexible, but the TolB box of 5 residues (DGSGW) is organised within this disordered domain<ref> PMID: 15452437 </ref>. Within this pentapeptide sequence, the 3 essential resides are D35, S37 and W39. Mutations in all but one of these residues leads to a reduced affinity of binding to TolB<ref> PMID: 16166536 </ref>. Some regions in the entire site have reduced mobility relative to other regions, that form local hydrophobic clusters<ref> PMID: 15452437 </ref>.

Gemma McGoldrick: /* Synthesis and release */

Gemma McGoldrick — Sat, 26 Feb 2011 15:21:20 GMT

Synthesis and release

←Older revision		Revision as of 15:21, 26 February 2011
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	==Synthesis and release==		==Synthesis and release==
	{{STRUCTURE_1emv \| PDB=1emv \| SCENE= Colicin_E9/Cole9dnaseim9/1 }}		{{STRUCTURE_1emv \| PDB=1emv \| SCENE= Colicin_E9/Cole9dnaseim9/1 }}
-	Colicin E9 in solution, ie in the cytoplasm after synthesis, is monomeric, and forms a high affinity complex with its immunity protein, [[Im9]]. The immunity protein does not directly bind to the active site, but instead to an exosite. This is bound while in the producing cell to protect it from the activity<ref> PMID: 15044477 </ref>. The structure shown is that of the <scene name='Colicin_E9/Cole9dnas/1'>DNase domain</scene> of colicin E9 bound to Im9<ref> PMID: 10966813 </ref>.	+	Colicin E9 in solution, ie in the cytoplasm after synthesis, is monomeric, and forms a high affinity complex with its immunity protein, [[Im9]]. The immunity protein does not directly bind to the active site, but instead to an exosite. This is bound while in the producing cell to protect it from the activity<ref> PMID: 15044477 </ref>. The structure shown is that of the <scene name='Colicin_E9/Cole9dnas/1'>DNase domain</scene> of colicin E9 bound to <scene name='Colicin_E9/Im9/2'>Im9</scene><ref> PMID: 10966813 </ref>.

	==Mechanism of uptake==		==Mechanism of uptake==

Gemma McGoldrick: /* Synthesis and release */

Gemma McGoldrick — Sat, 26 Feb 2011 15:14:09 GMT

Synthesis and release

←Older revision		Revision as of 15:14, 26 February 2011
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	==Synthesis and release==		==Synthesis and release==
	{{STRUCTURE_1emv \| PDB=1emv \| SCENE= Colicin_E9/Cole9dnaseim9/1 }}		{{STRUCTURE_1emv \| PDB=1emv \| SCENE= Colicin_E9/Cole9dnaseim9/1 }}
-	Colicin E9 in solution, ie in the cytoplasm after synthesis, is monomeric, and forms a high affinity complex with its immunity protein, [[Im9]]. The immunity protein does not directly bind to the active site, but instead to an exosite. This is bound while in the producing cell to protect it from the activity<ref> PMID: 15044477 </ref>. The structure shown is that of the DNase domain of colicin E9 bound to Im9<ref> PMID: 10966813 </ref>.	+	Colicin E9 in solution, ie in the cytoplasm after synthesis, is monomeric, and forms a high affinity complex with its immunity protein, [[Im9]]. The immunity protein does not directly bind to the active site, but instead to an exosite. This is bound while in the producing cell to protect it from the activity<ref> PMID: 15044477 </ref>. The structure shown is that of the <scene name='Colicin_E9/Cole9dnas/1'>DNase domain</scene> of colicin E9 bound to Im9<ref> PMID: 10966813 </ref>.

	==Mechanism of uptake==		==Mechanism of uptake==

Gemma McGoldrick: /* Synthesis and release */

Gemma McGoldrick — Fri, 25 Feb 2011 13:35:58 GMT

Synthesis and release

←Older revision		Revision as of 13:35, 25 February 2011
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	==Synthesis and release==		==Synthesis and release==
-	{{STRUCTURE_1emv \| PDB=1emv \| SCENE= }}	+	{{STRUCTURE_1emv \| PDB=1emv \| SCENE= Colicin_E9/Cole9dnaseim9/1 }}
	Colicin E9 in solution, ie in the cytoplasm after synthesis, is monomeric, and forms a high affinity complex with its immunity protein, [[Im9]]. The immunity protein does not directly bind to the active site, but instead to an exosite. This is bound while in the producing cell to protect it from the activity<ref> PMID: 15044477 </ref>. The structure shown is that of the DNase domain of colicin E9 bound to Im9<ref> PMID: 10966813 </ref>.		Colicin E9 in solution, ie in the cytoplasm after synthesis, is monomeric, and forms a high affinity complex with its immunity protein, [[Im9]]. The immunity protein does not directly bind to the active site, but instead to an exosite. This is bound while in the producing cell to protect it from the activity<ref> PMID: 15044477 </ref>. The structure shown is that of the DNase domain of colicin E9 bound to Im9<ref> PMID: 10966813 </ref>.

Gemma McGoldrick: /* Killing Activities */

Gemma McGoldrick — Mon, 07 Feb 2011 09:33:32 GMT

Killing Activities

←Older revision		Revision as of 09:33, 7 February 2011
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	The DNase domain nicks dsDNA at thymine bases<ref> PMID: 15995205 </ref>.		The DNase domain nicks dsDNA at thymine bases<ref> PMID: 15995205 </ref>.

-	The catalytic centre of the DNase domain contains the [[H-N-H motif]], a site for DNA and metal binding. ColE9 binds Mg<sup>2+</sup> as its cofactor<ref> PMID: 12136104 </ref>. Binding the magnesium ion stabilises the protein<ref> PMID: 15044477 </ref>, and regulates the binding of phosphate ions to the active site. Upon binding to the ion, the conformation of the DNase alters. This diagram shows the ~~binding of the metal ion and the phosphate to the DNase domain~~<ref> PMID: ~~15726170~~ </ref>.	+	The catalytic centre of the DNase domain contains the [[H-N-H motif]], a site for DNA and metal binding. ColE9 binds Mg<sup>2+</sup> as its cofactor<ref> PMID: 12136104 </ref>. Binding the magnesium ion stabilises the protein<ref> PMID: 15044477 </ref>, and regulates the binding of phosphate ions to the active site. Upon binding to the ion, the conformation of the DNase alters. This diagram shows the HNH motif found in ColE9<ref> PMID: 17516660 </ref>.

	[[Image:HNH domain of colE9 17516660.png]]		[[Image:HNH domain of colE9 17516660.png]]

Gemma McGoldrick at 09:32, 7 February 2011

Gemma McGoldrick — Mon, 07 Feb 2011 09:32:50 GMT

←Older revision		Revision as of 09:32, 7 February 2011
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	The catalytic centre of the DNase domain contains the [[H-N-H motif]], a site for DNA and metal binding. ColE9 binds Mg<sup>2+</sup> as its cofactor<ref> PMID: 12136104 </ref>. Binding the magnesium ion stabilises the protein<ref> PMID: 15044477 </ref>, and regulates the binding of phosphate ions to the active site. Upon binding to the ion, the conformation of the DNase alters. This diagram shows the binding of the metal ion and the phosphate to the DNase domain<ref> PMID: 15726170 </ref>.		The catalytic centre of the DNase domain contains the [[H-N-H motif]], a site for DNA and metal binding. ColE9 binds Mg<sup>2+</sup> as its cofactor<ref> PMID: 12136104 </ref>. Binding the magnesium ion stabilises the protein<ref> PMID: 15044477 </ref>, and regulates the binding of phosphate ions to the active site. Upon binding to the ion, the conformation of the DNase alters. This diagram shows the binding of the metal ion and the phosphate to the DNase domain<ref> PMID: 15726170 </ref>.

-	[[Image:~~From_15726170~~.png]]	+	[[Image:HNH domain of colE9 17516660.png]]

	In response to the DNA damage by colE9, the ''E. coli'' cell initiates an SOS response, prior to cell death<ref> PMID: 15044477 </ref>. This involves the strong induction of 28 genes of the LexA-regulated SOS response<ref> PMID: 15995205 </ref>.		In response to the DNA damage by colE9, the ''E. coli'' cell initiates an SOS response, prior to cell death<ref> PMID: 15044477 </ref>. This involves the strong induction of 28 genes of the LexA-regulated SOS response<ref> PMID: 15995205 </ref>.