6luv - Revision history

OCA at 14:55, 29 November 2023

OCA — Wed, 29 Nov 2023 14:55:11 GMT

←Older revision		Revision as of 14:55, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='6luv' size='340' side='right'caption='[[6luv]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='6luv' size='340' side='right'caption='[[6luv]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6luv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LUV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6luv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LUV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CO2:CARBON+DIOXIDE'>CO2</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[6luu\|6luu]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CA2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6luv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6luv OCA], [https://pdbe.org/6luv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6luv RCSB], [https://www.ebi.ac.uk/pdbsum/6luv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6luv ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6luv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6luv OCA], [https://pdbe.org/6luv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6luv RCSB], [https://www.ebi.ac.uk/pdbsum/6luv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6luv ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[https://omim.org/entry/259730 259730]]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>	+	[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[https://omim.org/entry/259730 259730]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>	+	[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6luv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6luv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carbonic anhydrase 3D structures\|Carbonic anhydrase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Carbonate dehydratase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim~~, C U~~]]	+	[[Category: Kim CU]]
-	[[Category: Kim~~, J K]]~~	+	[[Category: Kim JK]]
-	~~[[Category: Biological water dynamic]]~~	+
-	~~[[Category: Carbonic anhydrase]]~~	+
-	~~[[Category: Enzyme mechanism]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Metal coordination geometry]]~~	+
-	~~[[Category: Metalloenzyme]]~~	+
-	~~[[Category: Proton transfer~~]]	+

OCA at 14:53, 3 March 2021

OCA — Wed, 03 Mar 2021 14:53:28 GMT

←Older revision		Revision as of 14:53, 3 March 2021
Line 1:		Line 1:

	==apo- Carbonic Anhydrase II pH 7.8 20 atm CO2==		==apo- Carbonic Anhydrase II pH 7.8 20 atm CO2==
-	<StructureSection load='6luv' size='340' side='right'caption='[[6luv]]' scene=''>	+	<StructureSection load='6luv' size='340' side='right'caption='[[6luv]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LUV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LUV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6luv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LUV FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6luv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6luv OCA], [~~http~~://pdbe.org/6luv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6luv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6luv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6luv ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6luu\|6luu]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CA2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6luv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6luv OCA], [https://pdbe.org/6luv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6luv RCSB], [https://www.ebi.ac.uk/pdbsum/6luv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6luv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[https://omim.org/entry/259730 259730]]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Why metalloenzymes often show dramatic changes in their catalytic activity when subjected to chemically similar but non-native metal substitutions is a long-standing puzzle. Here, we report on the catalytic roles of metal ions in a model metalloenzyme system, human carbonic anhydrase II (CA II). Through a comparative study on the intermediate states of the zinc-bound native CA II and non-native metal-substituted CA IIs, we demonstrate that the characteristic metal ion coordination geometries (tetrahedral for Zn(2+), tetrahedral to octahedral conversion for Co(2+), octahedral for Ni(2+), and trigonal bipyramidal for Cu(2+)) directly modulate the catalytic efficacy. In addition, we reveal that the metal ions have a long-range (~10 A) electrostatic effect on restructuring water network in the active site. Our study provides evidence that the metal ions in metalloenzymes have a crucial impact on the catalytic mechanism beyond their primary chemical properties.
		+
		+	Elucidating the role of metal ions in carbonic anhydrase catalysis.,Kim JK, Lee C, Lim SW, Adhikari A, Andring JT, McKenna R, Ghim CM, Kim CU Nat Commun. 2020 Sep 11;11(1):4557. doi: 10.1038/s41467-020-18425-5. PMID:32917908<ref>PMID:32917908</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6luv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Carbonate dehydratase]]
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim CU]]	+	[[Category: Kim, C U]]
-	[[Category: Kim JK]]	+	[[Category: Kim, J K]]
		+	[[Category: Biological water dynamic]]
		+	[[Category: Carbonic anhydrase]]
		+	[[Category: Enzyme mechanism]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Metal coordination geometry]]
		+	[[Category: Metalloenzyme]]
		+	[[Category: Proton transfer]]

OCA at 06:17, 19 August 2020

OCA — Wed, 19 Aug 2020 06:17:46 GMT

←Older revision		Revision as of 06:17, 19 August 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6luv ~~is ON HOLD until Paper Publication~~	+	==apo- Carbonic Anhydrase II pH 7.8 20 atm CO2==
-		+	<StructureSection load='6luv' size='340' side='right'caption='[[6luv]]' scene=''>
-	~~Authors~~: ~~Kim~~, C.U., ~~Kim~~, J.K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LUV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LUV FirstGlance]. <br>
-	~~Description~~: ~~apo~~-~~Carbonic Anhydrase II pH 7~~.~~8 20 atm CO2~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6luv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6luv OCA], [http://pdbe.org/6luv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6luv RCSB], [http://www.ebi.ac.uk/pdbsum/6luv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6luv ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Kim~~, J.K~~]]	+	__TOC__
-	[[Category: Kim~~, C.U~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kim CU]]
		+	[[Category: Kim JK]]

OCA at 05:07, 19 February 2020

OCA — Wed, 19 Feb 2020 05:07:38 GMT

←Older revision		Revision as of 05:07, 19 February 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6luv is ON HOLD	+	The entry 6luv is ON HOLD until Paper Publication

	Authors: Kim, C.U., Kim, J.K.		Authors: Kim, C.U., Kim, J.K.

OCA: Protected "6luv" [edit=sysop:move=sysop]

OCA — Thu, 13 Feb 2020 02:31:44 GMT

Protected "6luv" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:31, 13 February 2020

OCA: New page: '''Unreleased structure''' The entry 6luv is ON HOLD Authors: Kim, C.U., Kim, J.K. Description: apo-Carbonic Anhydrase II pH 7.8 20 atm CO2 Category: Unreleased Structures [[Catego...

OCA — Thu, 13 Feb 2020 02:31:43 GMT

New page: '''Unreleased structure''' The entry 6luv is ON HOLD Authors: Kim, C.U., Kim, J.K. Description: apo-Carbonic Anhydrase II pH 7.8 20 atm CO2 Category: Unreleased Structures [[Catego...

New page

'''Unreleased structure'''

The entry 6luv is ON HOLD

Authors: Kim, C.U., Kim, J.K.

Description: apo-Carbonic Anhydrase II pH 7.8 20 atm CO2
[[Category: Unreleased Structures]]
[[Category: Kim, J.K]]
[[Category: Kim, C.U]]