User:Adam Kral/Sandbox 1 - Revision history

Adam Kral at 19:22, 23 May 2019

Adam Kral — Thu, 23 May 2019 19:22:21 GMT

←Older revision		Revision as of 19:22, 23 May 2019
Line 67:		Line 67:
	The other mutations usually distort the folding of the domain.		The other mutations usually distort the folding of the domain.
	Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>		Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>
		+	[[Image:SH3_BTK.png\|thumb\|SH3 domain with C-terminal deletion colored grey. PD BID: 1qly]]

	The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>		The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>

	Site-directed mutations of the polyproline II (PPII) helix forming proline residues in the PRRs of the TH domain of BTK abolish binding to SH3 domain. Mutations P189A and P192A are likely to alter the conformation such that the polyproline stretch can no longer be recognized. <ref name="vihinen99"/>		Site-directed mutations of the polyproline II (PPII) helix forming proline residues in the PRRs of the TH domain of BTK abolish binding to SH3 domain. Mutations P189A and P192A are likely to alter the conformation such that the polyproline stretch can no longer be recognized. <ref name="vihinen99"/>
-	~~[[Image:SH3_BTK.png\|thumb\|SH3 domain with C-terminal deletion colored grey. PD BID: 1qly]]~~	+

	===SH3 domain===		===SH3 domain===

Adam Kral at 19:20, 23 May 2019

Adam Kral — Thu, 23 May 2019 19:20:40 GMT

←Older revision		Revision as of 19:20, 23 May 2019
Line 60:		Line 60:
	Many mutations causing XLA were identified until today. It seems that most of them have evolved independently. They occur in all of the functional domains. Moreover, the distribution of mutations is quite uniform so that all the domains are affected almost equally. The kinase domain, for example, is comprising circa 40% of the length and accounts for about 45% of the mutations.		Many mutations causing XLA were identified until today. It seems that most of them have evolved independently. They occur in all of the functional domains. Moreover, the distribution of mutations is quite uniform so that all the domains are affected almost equally. The kinase domain, for example, is comprising circa 40% of the length and accounts for about 45% of the mutations.
	Approximately one third of the mutations are of the missense type and the rest consist of insertions, deletions, and nonsense and splice-site mutations. <ref name="saha97"/> Only a tiny fraction of the mutations is described in more detail here:		Approximately one third of the mutations are of the missense type and the rest consist of insertions, deletions, and nonsense and splice-site mutations. <ref name="saha97"/> Only a tiny fraction of the mutations is described in more detail here:
		+	[[Image:PH_BTK.png\|thumb\|Mutations in PH domain. Notice the residue Y40. PD BID: 4y93]]

	=== PH domain===		=== PH domain===
Line 66:		Line 67:
	The other mutations usually distort the folding of the domain.		The other mutations usually distort the folding of the domain.
	Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>		Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>
-	[[Image:PH_BTK.png\|thumb\|Mutations in PH domain. Notice the residue Y40. PD BID: 4y93]]

	The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>		The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>

	Site-directed mutations of the polyproline II (PPII) helix forming proline residues in the PRRs of the TH domain of BTK abolish binding to SH3 domain. Mutations P189A and P192A are likely to alter the conformation such that the polyproline stretch can no longer be recognized. <ref name="vihinen99"/>		Site-directed mutations of the polyproline II (PPII) helix forming proline residues in the PRRs of the TH domain of BTK abolish binding to SH3 domain. Mutations P189A and P192A are likely to alter the conformation such that the polyproline stretch can no longer be recognized. <ref name="vihinen99"/>
		+	[[Image:SH3_BTK.png\|thumb\|SH3 domain with C-terminal deletion colored grey. PD BID: 1qly]]

	===SH3 domain===		===SH3 domain===
	In SH3 domain, aberrant splicing and skipping of exon 9 leads to an in-frame deletion of 21 residues containing the 14 C-terminal residues of the SH3 domain. These are forming the last three ß-strands. Even though the aberrant protein is stable and has full kinase activity in vitro, the patients do have the disease. The deletion of those ß-strands seems to distort the structure but the spacing between the termini in the mutant protein corresponds to the normal BTK SH3 domain. Thus the connection to the rest of the BTK is normal and the deletion causes no major changes in the overall protein fold. <ref name="vihinen99"/>		In SH3 domain, aberrant splicing and skipping of exon 9 leads to an in-frame deletion of 21 residues containing the 14 C-terminal residues of the SH3 domain. These are forming the last three ß-strands. Even though the aberrant protein is stable and has full kinase activity in vitro, the patients do have the disease. The deletion of those ß-strands seems to distort the structure but the spacing between the termini in the mutant protein corresponds to the normal BTK SH3 domain. Thus the connection to the rest of the BTK is normal and the deletion causes no major changes in the overall protein fold. <ref name="vihinen99"/>
-	[[Image:~~SH3_BTK~~.png\|thumb\|~~SH3~~ domain with ~~C-terminal deletion colored grey~~. PD BID: ~~1qly~~]]	+	[[Image:Kinase BTK.png\|thumb\|Kinase domain with highlighted mutant sites. PD BID: 3p08]]
		+

	===Kinase domain===		===Kinase domain===
	Speaking about the kinase domain, there are several different types of missense mutations known, affecting structural, functional and interacting residues. The severe XLA mutations occur mainly in the ATP-binding region and the predicted substrate binding part. Some of them where found in other functionally or structurally important sites. Let the mutation A508D be one example of all. It introduces a charged residue in the hydrophobic core of the domain and, therefore, is likely to alter its conformation.		Speaking about the kinase domain, there are several different types of missense mutations known, affecting structural, functional and interacting residues. The severe XLA mutations occur mainly in the ATP-binding region and the predicted substrate binding part. Some of them where found in other functionally or structurally important sites. Let the mutation A508D be one example of all. It introduces a charged residue in the hydrophobic core of the domain and, therefore, is likely to alter its conformation.
	Other important sites, where mutation leads to XLA (residues 502, 506, 508 and 509), are located in alpha helix E of the lower lobe. Each of these seem to be critical for maintaining the proper overall structure. <ref name="saha97"/> <ref name="vihinen99"/>		Other important sites, where mutation leads to XLA (residues 502, 506, 508 and 509), are located in alpha helix E of the lower lobe. Each of these seem to be critical for maintaining the proper overall structure. <ref name="saha97"/> <ref name="vihinen99"/>
-	[[Image:Kinase BTK.png\|thumb\|Kinase domain with highlighted mutant sites. PD BID: 3p08]]

Adam Kral at 19:18, 23 May 2019

Adam Kral — Thu, 23 May 2019 19:18:18 GMT

←Older revision		Revision as of 19:18, 23 May 2019
Line 66:		Line 66:
	The other mutations usually distort the folding of the domain.		The other mutations usually distort the folding of the domain.
	Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>		Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>
-	[[Image:PH_BTK.png]\|thumb\|Mutations in PH domain. Notice the residue Y40. PD BID: 4y93]	+	[[Image:PH_BTK.png\|thumb\|Mutations in PH domain. Notice the residue Y40. PD BID: 4y93]]

	The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>		The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>
Line 74:		Line 74:
	===SH3 domain===		===SH3 domain===
	In SH3 domain, aberrant splicing and skipping of exon 9 leads to an in-frame deletion of 21 residues containing the 14 C-terminal residues of the SH3 domain. These are forming the last three ß-strands. Even though the aberrant protein is stable and has full kinase activity in vitro, the patients do have the disease. The deletion of those ß-strands seems to distort the structure but the spacing between the termini in the mutant protein corresponds to the normal BTK SH3 domain. Thus the connection to the rest of the BTK is normal and the deletion causes no major changes in the overall protein fold. <ref name="vihinen99"/>		In SH3 domain, aberrant splicing and skipping of exon 9 leads to an in-frame deletion of 21 residues containing the 14 C-terminal residues of the SH3 domain. These are forming the last three ß-strands. Even though the aberrant protein is stable and has full kinase activity in vitro, the patients do have the disease. The deletion of those ß-strands seems to distort the structure but the spacing between the termini in the mutant protein corresponds to the normal BTK SH3 domain. Thus the connection to the rest of the BTK is normal and the deletion causes no major changes in the overall protein fold. <ref name="vihinen99"/>
-	[[Image:SH3_BTK.png]\|thumb\|SH3 domain with C-terminal deletion colored grey. PD BID: 1qly]	+	[[Image:SH3_BTK.png\|thumb\|SH3 domain with C-terminal deletion colored grey. PD BID: 1qly]]

	===Kinase domain===		===Kinase domain===
	Speaking about the kinase domain, there are several different types of missense mutations known, affecting structural, functional and interacting residues. The severe XLA mutations occur mainly in the ATP-binding region and the predicted substrate binding part. Some of them where found in other functionally or structurally important sites. Let the mutation A508D be one example of all. It introduces a charged residue in the hydrophobic core of the domain and, therefore, is likely to alter its conformation.		Speaking about the kinase domain, there are several different types of missense mutations known, affecting structural, functional and interacting residues. The severe XLA mutations occur mainly in the ATP-binding region and the predicted substrate binding part. Some of them where found in other functionally or structurally important sites. Let the mutation A508D be one example of all. It introduces a charged residue in the hydrophobic core of the domain and, therefore, is likely to alter its conformation.
	Other important sites, where mutation leads to XLA (residues 502, 506, 508 and 509), are located in alpha helix E of the lower lobe. Each of these seem to be critical for maintaining the proper overall structure. <ref name="saha97"/> <ref name="vihinen99"/>		Other important sites, where mutation leads to XLA (residues 502, 506, 508 and 509), are located in alpha helix E of the lower lobe. Each of these seem to be critical for maintaining the proper overall structure. <ref name="saha97"/> <ref name="vihinen99"/>
-	[[Image:Kinase BTK.png]\|thumb\|Kinase domain with highlighted mutant sites. PD BID: 3p08]	+	[[Image:Kinase BTK.png\|thumb\|Kinase domain with highlighted mutant sites. PD BID: 3p08]]

Adam Kral at 19:16, 23 May 2019

Adam Kral — Thu, 23 May 2019 19:16:46 GMT

←Older revision		Revision as of 19:16, 23 May 2019
Line 66:		Line 66:
	The other mutations usually distort the folding of the domain.		The other mutations usually distort the folding of the domain.
	Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>		Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>
-	[[Image:PH_BTK.png]]	+	[[Image:PH_BTK.png]\|thumb\|Mutations in PH domain. Notice the residue Y40. PD BID: 4y93]

	The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>		The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>
Line 74:		Line 74:
	===SH3 domain===		===SH3 domain===
	In SH3 domain, aberrant splicing and skipping of exon 9 leads to an in-frame deletion of 21 residues containing the 14 C-terminal residues of the SH3 domain. These are forming the last three ß-strands. Even though the aberrant protein is stable and has full kinase activity in vitro, the patients do have the disease. The deletion of those ß-strands seems to distort the structure but the spacing between the termini in the mutant protein corresponds to the normal BTK SH3 domain. Thus the connection to the rest of the BTK is normal and the deletion causes no major changes in the overall protein fold. <ref name="vihinen99"/>		In SH3 domain, aberrant splicing and skipping of exon 9 leads to an in-frame deletion of 21 residues containing the 14 C-terminal residues of the SH3 domain. These are forming the last three ß-strands. Even though the aberrant protein is stable and has full kinase activity in vitro, the patients do have the disease. The deletion of those ß-strands seems to distort the structure but the spacing between the termini in the mutant protein corresponds to the normal BTK SH3 domain. Thus the connection to the rest of the BTK is normal and the deletion causes no major changes in the overall protein fold. <ref name="vihinen99"/>
-	[[Image:SH3_BTK.png]]	+	[[Image:SH3_BTK.png]\|thumb\|SH3 domain with C-terminal deletion colored grey. PD BID: 1qly]

	===Kinase domain===		===Kinase domain===
	Speaking about the kinase domain, there are several different types of missense mutations known, affecting structural, functional and interacting residues. The severe XLA mutations occur mainly in the ATP-binding region and the predicted substrate binding part. Some of them where found in other functionally or structurally important sites. Let the mutation A508D be one example of all. It introduces a charged residue in the hydrophobic core of the domain and, therefore, is likely to alter its conformation.		Speaking about the kinase domain, there are several different types of missense mutations known, affecting structural, functional and interacting residues. The severe XLA mutations occur mainly in the ATP-binding region and the predicted substrate binding part. Some of them where found in other functionally or structurally important sites. Let the mutation A508D be one example of all. It introduces a charged residue in the hydrophobic core of the domain and, therefore, is likely to alter its conformation.
	Other important sites, where mutation leads to XLA (residues 502, 506, 508 and 509), are located in alpha helix E of the lower lobe. Each of these seem to be critical for maintaining the proper overall structure. <ref name="saha97"/> <ref name="vihinen99"/>		Other important sites, where mutation leads to XLA (residues 502, 506, 508 and 509), are located in alpha helix E of the lower lobe. Each of these seem to be critical for maintaining the proper overall structure. <ref name="saha97"/> <ref name="vihinen99"/>
-	[[Image:Kinase BTK.png]]	+	[[Image:Kinase BTK.png]\|thumb\|Kinase domain with highlighted mutant sites. PD BID: 3p08]


Line 88:		Line 88:

	==Credits==		==Credits==
-	This article was created by Jan Keil, Barbora Kovandová, Adam Král and Linda Rendlová for Structural Biology of the Cell class, Charles University, summer 2019.	+	This article was created by Jan Keil, Barbora Kovandová, Adam Král and Linda Rendlová for Structural Biology of the Cell class, Charles University, summer 2019. (PyMol software used to create the images)

Adam Kral at 19:07, 23 May 2019

Adam Kral — Thu, 23 May 2019 19:07:59 GMT

←Older revision		Revision as of 19:07, 23 May 2019
Line 66:		Line 66:
	The other mutations usually distort the folding of the domain.		The other mutations usually distort the folding of the domain.
	Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>		Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>
-	[[Image:PH_BTK]]	+	[[Image:PH_BTK.png]]

	The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>		The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>

Adam Kral at 19:05, 23 May 2019

Adam Kral — Thu, 23 May 2019 19:05:29 GMT

←Older revision		Revision as of 19:05, 23 May 2019
Line 66:		Line 66:
	The other mutations usually distort the folding of the domain.		The other mutations usually distort the folding of the domain.
	Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>		Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>
-	[[Image:~~PH BTK~~]]	+	[[Image:PH_BTK]]

	The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>		The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>

Adam Kral at 19:02, 23 May 2019

Adam Kral — Thu, 23 May 2019 19:02:40 GMT

←Older revision		Revision as of 19:02, 23 May 2019
Line 66:		Line 66:
	The other mutations usually distort the folding of the domain.		The other mutations usually distort the folding of the domain.
	Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>		Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>
-	[[Image:~~PH_BTK~~]]	+	[[Image:PH BTK]]

	The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>		The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>
Line 79:		Line 79:
	Speaking about the kinase domain, there are several different types of missense mutations known, affecting structural, functional and interacting residues. The severe XLA mutations occur mainly in the ATP-binding region and the predicted substrate binding part. Some of them where found in other functionally or structurally important sites. Let the mutation A508D be one example of all. It introduces a charged residue in the hydrophobic core of the domain and, therefore, is likely to alter its conformation.		Speaking about the kinase domain, there are several different types of missense mutations known, affecting structural, functional and interacting residues. The severe XLA mutations occur mainly in the ATP-binding region and the predicted substrate binding part. Some of them where found in other functionally or structurally important sites. Let the mutation A508D be one example of all. It introduces a charged residue in the hydrophobic core of the domain and, therefore, is likely to alter its conformation.
	Other important sites, where mutation leads to XLA (residues 502, 506, 508 and 509), are located in alpha helix E of the lower lobe. Each of these seem to be critical for maintaining the proper overall structure. <ref name="saha97"/> <ref name="vihinen99"/>		Other important sites, where mutation leads to XLA (residues 502, 506, 508 and 509), are located in alpha helix E of the lower lobe. Each of these seem to be critical for maintaining the proper overall structure. <ref name="saha97"/> <ref name="vihinen99"/>
-	[[Image:PH BTK.png]]	+	[[Image:Kinase BTK.png]]

Adam Kral at 18:58, 23 May 2019

Adam Kral — Thu, 23 May 2019 18:58:25 GMT

←Older revision		Revision as of 18:58, 23 May 2019
Line 66:		Line 66:
	The other mutations usually distort the folding of the domain.		The other mutations usually distort the folding of the domain.
	Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>		Y40 is one of the other sites, which are probably critical for normal function of the PH domain, maintaining its structural stability and participating on IP binding. The Y40N and Y40C mutations both cause a loss-of-function phenotype in XLA and seems to result in a significantly low affinity for IP4. <ref name="saha97"/><ref name="vihinen99"/>
		+	[[Image:PH_BTK]]

	The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>		The structural model of the PH domain <!--todo add [[Image:]]-->, shows these residues, along with Y40, cluster on the same plane of the binding site. The side chain of Y40 is buried by the loop between β-strands 3 and 4, and the hydroxyl group of Y40 could potentially form a hydrogen bond with the backbone of G50. Mutations at this site will probably have structural consequences on the conformation of the loop and the phosphatidylinositol binding site and maybe of the whole domain. Thus, they are likely to be damaging for the normal function of BTK. <ref name="saha97"/>
Line 78:		Line 79:
	Speaking about the kinase domain, there are several different types of missense mutations known, affecting structural, functional and interacting residues. The severe XLA mutations occur mainly in the ATP-binding region and the predicted substrate binding part. Some of them where found in other functionally or structurally important sites. Let the mutation A508D be one example of all. It introduces a charged residue in the hydrophobic core of the domain and, therefore, is likely to alter its conformation.		Speaking about the kinase domain, there are several different types of missense mutations known, affecting structural, functional and interacting residues. The severe XLA mutations occur mainly in the ATP-binding region and the predicted substrate binding part. Some of them where found in other functionally or structurally important sites. Let the mutation A508D be one example of all. It introduces a charged residue in the hydrophobic core of the domain and, therefore, is likely to alter its conformation.
	Other important sites, where mutation leads to XLA (residues 502, 506, 508 and 509), are located in alpha helix E of the lower lobe. Each of these seem to be critical for maintaining the proper overall structure. <ref name="saha97"/> <ref name="vihinen99"/>		Other important sites, where mutation leads to XLA (residues 502, 506, 508 and 509), are located in alpha helix E of the lower lobe. Each of these seem to be critical for maintaining the proper overall structure. <ref name="saha97"/> <ref name="vihinen99"/>
		+	[[Image:PH BTK.png]]

Adam Kral at 18:50, 23 May 2019

Adam Kral — Thu, 23 May 2019 18:50:05 GMT

←Older revision		Revision as of 18:50, 23 May 2019
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	===SH3 domain===		===SH3 domain===
	In SH3 domain, aberrant splicing and skipping of exon 9 leads to an in-frame deletion of 21 residues containing the 14 C-terminal residues of the SH3 domain. These are forming the last three ß-strands. Even though the aberrant protein is stable and has full kinase activity in vitro, the patients do have the disease. The deletion of those ß-strands seems to distort the structure but the spacing between the termini in the mutant protein corresponds to the normal BTK SH3 domain. Thus the connection to the rest of the BTK is normal and the deletion causes no major changes in the overall protein fold. <ref name="vihinen99"/>		In SH3 domain, aberrant splicing and skipping of exon 9 leads to an in-frame deletion of 21 residues containing the 14 C-terminal residues of the SH3 domain. These are forming the last three ß-strands. Even though the aberrant protein is stable and has full kinase activity in vitro, the patients do have the disease. The deletion of those ß-strands seems to distort the structure but the spacing between the termini in the mutant protein corresponds to the normal BTK SH3 domain. Thus the connection to the rest of the BTK is normal and the deletion causes no major changes in the overall protein fold. <ref name="vihinen99"/>
		+	[[Image:SH3_BTK.png]]

	===Kinase domain===		===Kinase domain===

Adam Kral at 06:03, 17 May 2019

Adam Kral — Fri, 17 May 2019 06:03:41 GMT

←Older revision		Revision as of 06:03, 17 May 2019
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	BTK consists of five functional domains. These are PH (Pleckstrin homology), TH (Tec homology), SH3, SH2 (Src homology) and C-terminal kinase domain. This composition is a typical feature of the Tec family of cytosolic protein tyrosine kinases, where BTK belongs. <ref name="saha97"/> Now, a brief characterisation of each domain follows:		BTK consists of five functional domains. These are PH (Pleckstrin homology), TH (Tec homology), SH3, SH2 (Src homology) and C-terminal kinase domain. This composition is a typical feature of the Tec family of cytosolic protein tyrosine kinases, where BTK belongs. <ref name="saha97"/> Now, a brief characterisation of each domain follows:
	====PH domain====		====PH domain====
-	Tec family kinases are the only Tyrosine kinases, that ~~contains~~ a PH domain. Besides, PH domain is present in various proteins involved in signalisation, such as phospholipase C or GTPase activating proteins. There is a low sequence similarity between PH domains in various proteins, however they all share similar fold. With the length of 131 amino acids in BTK, it is the second largest domain. The N terminal part (namely the three conserved lysines) is responsible for binding phosphoinositides and leading them to its targeting to the plasma membrane, where it activates the NF-kappaB complex. The C terminus, together with the following TH domain plays a role in binding ßgamma subunits of heterotrimeric G proteins. <ref name="uniprotkb19"/> <ref name="vihinen99"/>	+	Tec family kinases are the only Tyrosine kinases, that contain a PH domain. Besides, PH domain is present in various proteins involved in signalisation, such as phospholipase C or GTPase activating proteins. There is a low sequence similarity between PH domains in various proteins, however they all share similar fold. With the length of 131 amino acids in BTK, it is the second largest domain. The N terminal part (namely the three conserved lysines) is responsible for binding phosphoinositides and leading them to its targeting to the plasma membrane, where it activates the NF-kappaB complex. The C terminus, together with the following TH domain plays a role in binding ßgamma subunits of heterotrimeric G proteins. <ref name="uniprotkb19"/> <ref name="vihinen99"/>

	====TH domain====		====TH domain====