JMS/sandbox4 - Revision history

Joseph M. Steinberger at 12:31, 4 September 2012

Joseph M. Steinberger — Tue, 04 Sep 2012 12:31:01 GMT

←Older revision		Revision as of 12:31, 4 September 2012
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	<StructureSection load='1Y7W' size='350' side='right' caption='Structure of alpha-type carbonic anhydrase (dCAII) (PDB entry [[1Y7W]])' scene='JMS/sandbox4/Ca/3'>		<StructureSection load='1Y7W' size='350' side='right' caption='Structure of alpha-type carbonic anhydrase (dCAII) (PDB entry [[1Y7W]])' scene='JMS/sandbox4/Ca/3'>

-	The halotolerant carbonic anhydrase (dCAII) looks like other carbonic anhydrases, showing high structural similarity. But looks aside, dCAII has an unusual ability to weather extreme environments.<ref>PMID:15894606</ref>	+	The halotolerant carbonic anhydrase (dCAII) looks like other carbonic anhydrases (CA), showing high structural similarity. But looks aside, dCAII has an unusual ability to weather extreme environments.<ref>PMID:15894606</ref>

-	Carbonic anhydrases are enzymes which catalyze the interconversion of CO2 and water to bicarbonate and proton. For ~~full~~ entry on γ-carbonic anhydrase see [[Gamma Carbonic Anhydrase]].	+	Carbonic anhydrases are enzymes which catalyze the interconversion of CO2 and water to bicarbonate and proton. For a complementary entry on carbonic anhydrases, and specifically γ-carbonic anhydrase, the class which included dCAII, see [[Gamma Carbonic Anhydrase]].

-	dCAII has the <scene name='JMS/sandbox4/Ca/3'>general structure of CA</scene>, such as:	+	dCAII has a decidedly unusual ability to function both in extremely high salt concentrations, and, also, in low salt concentrations.This dual nature results from dCAII well-calibrated amount of negative surface. The <scene name='JMS/sandbox4/Surface/2'> negative surface</scene> prevents misfolding in highly salty environments. But the surface is not so negative that dCAII requires lots of salt to function. Meaning, dCAII is rather negative, but not as negative as halophiles. Therein lies the difference between Halo''phile'' and Halo''tolerant''.
		+
		+	Despite dCAII's unusual chemical properties, dCAII has the <scene name='JMS/sandbox4/Ca/3'>general structure of CA</scene>, such as:

	<font color='orange'><b>two prominent alpha helixes</b></font> (here, the two ''longest'' helixes)		<font color='orange'><b>two prominent alpha helixes</b></font> (here, the two ''longest'' helixes)
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-	In the following <scene name='1y7w/Com_view/8'>conserved region illustration</scene> of the carbonic anhydrase from ''Dunaliella salina'' (~~dCA II~~) structure. The regions corresponding to conserved regions <font color='blue'><b>(CRs, blue)</b></font>, variable regions <font color='lime'><b>(VRs, lime)</b></font>, and variable conserved regions <font color='red'><b>(VCRs, red)</b></font>, are positioned on the dCA II structure. The catalytic Zn<sup>2+</sup>, insertions and deletions in VCRs including L1 (the Zn binding loop), L4 (the Na-binding loop), L5, and two extended α-helices (E and G) are marked. N and C termini are labeled.	+	In the following <scene name='1y7w/Com_view/8'>conserved region illustration</scene> of the carbonic anhydrase from ''Dunaliella salina'' (dCAII) structure. The regions corresponding to conserved regions <font color='blue'><b>(CRs, blue)</b></font>, variable regions <font color='lime'><b>(VRs, lime)</b></font>, and variable conserved regions <font color='red'><b>(VCRs, red)</b></font>, are positioned on the dCA II structure. The catalytic Zn<sup>2+</sup>, insertions and deletions in VCRs including L1 (the Zn binding loop), L4 (the Na-binding loop), L5, and two extended α-helices (E and G) are marked. N and C termini are labeled.
-		+
-		+
-	Still, dCAII has a decidedly unusual ability to function in extremely high salt concentrations, but, also, in low salt concentrations.This balance comes from a predominantly <scene name='JMS/sandbox4/Surface/2'> negative surface</scene> negative surface, on the one hand, that is still less negative than that observed in halophiles, on the other hand. Therein lies the difference between Halo''phile'' and Halo''tolerant''.	+
-		+

-	In summary, dCAII has ~~all the~~ properties of CA, ~~and strikes~~ the balance between positive and negative surface residues, which leads to ''tolerance'' of extremely salty conditions~~, and an ability to function in low salt conditions, as well~~.	+	In summary, dCAII has shares structural properties of CA, yet still manages to strike the balance between positive and negative surface residues, which leads to ''tolerance'' of extremely salty conditions.
	</StructureSection>		</StructureSection>
	<references/>		<references/>

Joseph M. Steinberger at 12:19, 4 September 2012

Joseph M. Steinberger — Tue, 04 Sep 2012 12:19:41 GMT

←Older revision		Revision as of 12:19, 4 September 2012
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	<StructureSection load='1Y7W' size='350' side='right' caption='Structure of alpha-type carbonic anhydrase (dCAII) (PDB entry [[1Y7W]])' scene='JMS/sandbox4/Ca/3'>		<StructureSection load='1Y7W' size='350' side='right' caption='Structure of alpha-type carbonic anhydrase (dCAII) (PDB entry [[1Y7W]])' scene='JMS/sandbox4/Ca/3'>

-	The halotolerant carbonic anhydrase (dCAII) ~~possesses~~ an unusual ability to weather extreme environments~~, still it displays much structural similarity to carbonic anhydrases (CA), generally~~.<ref>PMID:15894606</ref>	+	The halotolerant carbonic anhydrase (dCAII) looks like other carbonic anhydrases, showing high structural similarity. But looks aside, dCAII has an unusual ability to weather extreme environments.<ref>PMID:15894606</ref>

	Carbonic anhydrases are enzymes which catalyze the interconversion of CO2 and water to bicarbonate and proton. For full entry on γ-carbonic anhydrase see [[Gamma Carbonic Anhydrase]].		Carbonic anhydrases are enzymes which catalyze the interconversion of CO2 and water to bicarbonate and proton. For full entry on γ-carbonic anhydrase see [[Gamma Carbonic Anhydrase]].

Joseph M. Steinberger at 11:27, 9 August 2012

Joseph M. Steinberger — Thu, 09 Aug 2012 11:27:42 GMT

←Older revision		Revision as of 11:27, 9 August 2012
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	dCAII has the <scene name='JMS/sandbox4/Ca/3'>general structure of CA</scene>, such as:		dCAII has the <scene name='JMS/sandbox4/Ca/3'>general structure of CA</scene>, such as:

-	<font color='orange'><b>two prominent alpha helixes</b></font>~~orange: two prominent alpha helixes~~ (here, the two ''longest'' helixes)	+	<font color='orange'><b>two prominent alpha helixes</b></font> (here, the two ''longest'' helixes)
		+	<font color='green'><b>10 beta sheets</b></font>
		+	<span style="color:yellow;background-color:black;font-weight:bold;">catalytic zinc</span>

-	<font color='green'><b>10 beta sheets</b></font>green: 10 beta sheets
-
-	<span style="color:yellow;background-color:black;font-weight:bold;">catalytic zinc
-	</span>yellow: catalytic zinc

	dCAII has, too, the CA's <scene name='JMS/sandbox4/Active/2'>active site</scene> architectural elements.		dCAII has, too, the CA's <scene name='JMS/sandbox4/Active/2'>active site</scene> architectural elements.

-	<span style="color:pink;background-color:black;font-weight:bold;">Catalytic zinc coordinating residues	+	<span style="color:pink;background-color:black;font-weight:bold;">Catalytic zinc coordinating residues</span>
-	</span>~~: Catalytic zinc coordinating residues~~	+	<font color='red'><b>substrate binding</b></font>
		+	<font color='purple'><b>hydrogen binding</b></font>
		+	<font color='#20d0f0'><b>lacetate</b></font>

-	<font color='red'><b>substrate binding</b></font>: substrate binding

-	<font color='~~purple~~'><b>~~hydrogen binding~~</b></font>~~: hydrogen~~ binding	+	In the following <scene name='1y7w/Com_view/8'>conserved region illustration</scene> of the carbonic anhydrase from ''Dunaliella salina'' (dCA II) structure. The regions corresponding to conserved regions <font color='blue'><b>(CRs, blue)</b></font>, variable regions <font color='lime'><b>(VRs, lime)</b></font>, and variable conserved regions <font color='red'><b>(VCRs, red)</b></font>, are positioned on the dCA II structure. The catalytic Zn<sup>2+</sup>, insertions and deletions in VCRs including L1 (the Zn binding loop), L4 (the Na-binding loop), L5, and two extended α-helices (E and G) are marked. N and C termini are labeled.

-	<font color='#20d0f0'><b>lacetate</b></font>light-blue:acetate =

-	~~In the following~~ <scene name='~~1y7w~~/~~Com_view~~/8'>~~conserved region illustration~~</scene> of the ~~carbonic anhydrase from~~ ''~~Dunaliella salina~~'' ~~(dCA II) structure. The regions corresponding to conserved regions <font color=~~'~~blue~~'~~><b>(CRs, blue)</b></font>, variable regions <font color=~~'~~lime~~'><b>(VRs, lime)</b></font>, and variable conserved regions <font color='red'><b>(VCRs, red)</b></font>, are positioned on the dCA II structure. The catalytic Zn<sup>2+</sup>, insertions and deletions in VCRs including L1 (the Zn binding loop), L4 (the Na-binding loop), L5, and two extended α-helices (E and G) are marked. N and C termini are labeled.	+	Still, dCAII has a decidedly unusual ability to function in extremely high salt concentrations, but, also, in low salt concentrations.This balance comes from a predominantly <scene name='JMS/sandbox4/Surface/2'> negative surface</scene> negative surface, on the one hand, that is still less negative than that observed in halophiles, on the other hand. Therein lies the difference between Halo''phile'' and Halo''tolerant''.

-	Still, dCAII has a decidedly unusual ability to function in extremely high salt concentrations, but, also, in low salt concentrations.This balance comes from a predominantly <scene name='JMS/sandbox4/Surface/2'> negative surface</scene> negative surface, on the one hand, that is still less negative than that observed in halophiles, on the other hand. Therein lies the difference between Halo''phile'' and Halo''tolerant''.

	In summary, dCAII has all the properties of CA, and strikes the balance between positive and negative surface residues, which leads to ''tolerance'' of extremely salty conditions, and an ability to function in low salt conditions, as well.		In summary, dCAII has all the properties of CA, and strikes the balance between positive and negative surface residues, which leads to ''tolerance'' of extremely salty conditions, and an ability to function in low salt conditions, as well.
	</StructureSection>		</StructureSection>
	<references/>		<references/>

Joseph M. Steinberger at 11:23, 9 August 2012

Joseph M. Steinberger — Thu, 09 Aug 2012 11:23:41 GMT

←Older revision		Revision as of 11:23, 9 August 2012
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	dCAII has the <scene name='JMS/sandbox4/Ca/3'>general structure of CA</scene>, such as:		dCAII has the <scene name='JMS/sandbox4/Ca/3'>general structure of CA</scene>, such as:

-	<font color='orange'><b>~~substrate binding~~</b></font>orange: two prominent alpha helixes (here, the two ''longest'' helixes)	+	<font color='orange'><b>two prominent alpha helixes</b></font>orange: two prominent alpha helixes (here, the two ''longest'' helixes)

-	<font color='green'><b>~~substrate binding~~</b></font>green: 10 beta sheets	+	<font color='green'><b>10 beta sheets</b></font>green: 10 beta sheets

-	<span style="color:yellow;background-color:black;font-weight:bold;">~~Catalytic~~ zinc ~~coordinating residues~~	+	<span style="color:yellow;background-color:black;font-weight:bold;">catalytic zinc
	</span>yellow: catalytic zinc		</span>yellow: catalytic zinc

Joseph M. Steinberger at 11:23, 9 August 2012

Joseph M. Steinberger — Thu, 09 Aug 2012 11:23:04 GMT

←Older revision		Revision as of 11:23, 9 August 2012
Line 8:		Line 8:
	dCAII has the <scene name='JMS/sandbox4/Ca/3'>general structure of CA</scene>, such as:		dCAII has the <scene name='JMS/sandbox4/Ca/3'>general structure of CA</scene>, such as:

-	orange: two prominent alpha helixes (here, the two ''longest'' helixes)	+	<font color='orange'><b>substrate binding</b></font>orange: two prominent alpha helixes (here, the two ''longest'' helixes)

-	green: 10 beta sheets	+	<font color='green'><b>substrate binding</b></font>green: 10 beta sheets

-	yellow: catalytic zinc	+	<span style="color:yellow;background-color:black;font-weight:bold;">Catalytic zinc coordinating residues
		+	</span>yellow: catalytic zinc

	dCAII has, too, the CA's <scene name='JMS/sandbox4/Active/2'>active site</scene> architectural elements.		dCAII has, too, the CA's <scene name='JMS/sandbox4/Active/2'>active site</scene> architectural elements.

Joseph M. Steinberger at 11:22, 9 August 2012

Joseph M. Steinberger — Thu, 09 Aug 2012 11:22:15 GMT

←Older revision		Revision as of 11:22, 9 August 2012
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	dCAII has, too, the CA's <scene name='JMS/sandbox4/Active/2'>active site</scene> architectural elements.		dCAII has, too, the CA's <scene name='JMS/sandbox4/Active/2'>active site</scene> architectural elements.

-	<span style="color:pink;background-color:black;font-weight:bold;">~~pink~~</span>: Catalytic zinc coordinating residues	+	<span style="color:pink;background-color:black;font-weight:bold;">Catalytic zinc coordinating residues
		+	</span>: Catalytic zinc coordinating residues

	<font color='red'><b>substrate binding</b></font>: substrate binding		<font color='red'><b>substrate binding</b></font>: substrate binding

Joseph M. Steinberger at 11:19, 9 August 2012

Joseph M. Steinberger — Thu, 09 Aug 2012 11:19:11 GMT

←Older revision		Revision as of 11:19, 9 August 2012
Line 18:		Line 18:
	<span style="color:pink;background-color:black;font-weight:bold;">pink</span>: Catalytic zinc coordinating residues		<span style="color:pink;background-color:black;font-weight:bold;">pink</span>: Catalytic zinc coordinating residues

-	red: substrate binding	+	<font color='red'><b>substrate binding</b></font>: substrate binding

-	purple: hydrogen binding	+	<font color='purple'><b>hydrogen binding</b></font>: hydrogen binding

-	light-blue:acetate	+	<font color='#20d0f0'><b>lacetate</b></font>light-blue:acetate =

	In the following <scene name='1y7w/Com_view/8'>conserved region illustration</scene> of the carbonic anhydrase from ''Dunaliella salina'' (dCA II) structure. The regions corresponding to conserved regions <font color='blue'><b>(CRs, blue)</b></font>, variable regions <font color='lime'><b>(VRs, lime)</b></font>, and variable conserved regions <font color='red'><b>(VCRs, red)</b></font>, are positioned on the dCA II structure. The catalytic Zn<sup>2+</sup>, insertions and deletions in VCRs including L1 (the Zn binding loop), L4 (the Na-binding loop), L5, and two extended α-helices (E and G) are marked. N and C termini are labeled.		In the following <scene name='1y7w/Com_view/8'>conserved region illustration</scene> of the carbonic anhydrase from ''Dunaliella salina'' (dCA II) structure. The regions corresponding to conserved regions <font color='blue'><b>(CRs, blue)</b></font>, variable regions <font color='lime'><b>(VRs, lime)</b></font>, and variable conserved regions <font color='red'><b>(VCRs, red)</b></font>, are positioned on the dCA II structure. The catalytic Zn<sup>2+</sup>, insertions and deletions in VCRs including L1 (the Zn binding loop), L4 (the Na-binding loop), L5, and two extended α-helices (E and G) are marked. N and C termini are labeled.

Joseph M. Steinberger at 09:56, 9 August 2012

Joseph M. Steinberger — Thu, 09 Aug 2012 09:56:39 GMT

←Older revision		Revision as of 09:56, 9 August 2012
Line 16:		Line 16:
	dCAII has, too, the CA's <scene name='JMS/sandbox4/Active/2'>active site</scene> architectural elements.		dCAII has, too, the CA's <scene name='JMS/sandbox4/Active/2'>active site</scene> architectural elements.

-	pink: Catalytic zinc coordinating residues	+	<span style="color:pink;background-color:black;font-weight:bold;">pink</span>: Catalytic zinc coordinating residues

	red: substrate binding		red: substrate binding

Joseph M. Steinberger at 14:55, 8 August 2012

Joseph M. Steinberger — Wed, 08 Aug 2012 14:55:46 GMT

←Older revision		Revision as of 14:55, 8 August 2012
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	== The Halotolerant Carbonic Anhydrase ==		== The Halotolerant Carbonic Anhydrase ==
	<StructureSection load='1Y7W' size='350' side='right' caption='Structure of alpha-type carbonic anhydrase (dCAII) (PDB entry [[1Y7W]])' scene='JMS/sandbox4/Ca/3'>		<StructureSection load='1Y7W' size='350' side='right' caption='Structure of alpha-type carbonic anhydrase (dCAII) (PDB entry [[1Y7W]])' scene='JMS/sandbox4/Ca/3'>
-	~~<ref>PMID:15894606</ref>~~	+
-	The halotolerant carbonic anhydrase (dCAII) possesses an unusual ability to weather extreme environments, still it displays much structural similarity to carbonic anhydrases (CA), generally.	+	The halotolerant carbonic anhydrase (dCAII) possesses an unusual ability to weather extreme environments, still it displays much structural similarity to carbonic anhydrases (CA), generally.<ref>PMID:15894606</ref>

	Carbonic anhydrases are enzymes which catalyze the interconversion of CO2 and water to bicarbonate and proton. For full entry on γ-carbonic anhydrase see [[Gamma Carbonic Anhydrase]].		Carbonic anhydrases are enzymes which catalyze the interconversion of CO2 and water to bicarbonate and proton. For full entry on γ-carbonic anhydrase see [[Gamma Carbonic Anhydrase]].

Joseph M. Steinberger at 14:54, 8 August 2012

Joseph M. Steinberger — Wed, 08 Aug 2012 14:54:44 GMT

←Older revision		Revision as of 14:54, 8 August 2012
Line 1:		Line 1:
	== The Halotolerant Carbonic Anhydrase ==		== The Halotolerant Carbonic Anhydrase ==
	<StructureSection load='1Y7W' size='350' side='right' caption='Structure of alpha-type carbonic anhydrase (dCAII) (PDB entry [[1Y7W]])' scene='JMS/sandbox4/Ca/3'>		<StructureSection load='1Y7W' size='350' side='right' caption='Structure of alpha-type carbonic anhydrase (dCAII) (PDB entry [[1Y7W]])' scene='JMS/sandbox4/Ca/3'>
-	<ref>PMID:~~10.1073~~</ref>	+	<ref>PMID:15894606</ref>
	The halotolerant carbonic anhydrase (dCAII) possesses an unusual ability to weather extreme environments, still it displays much structural similarity to carbonic anhydrases (CA), generally.		The halotolerant carbonic anhydrase (dCAII) possesses an unusual ability to weather extreme environments, still it displays much structural similarity to carbonic anhydrases (CA), generally.