5dso - Revision history

OCA at 21:57, 28 June 2023

OCA — Wed, 28 Jun 2023 21:57:45 GMT

←Older revision		Revision as of 21:57, 28 June 2023
Line 1:		Line 1:

	==Structure of CO2 bound apo-form of human carbonic anhydrase II with 0 sec (no) warming==		==Structure of CO2 bound apo-form of human carbonic anhydrase II with 0 sec (no) warming==
-	<StructureSection load='5dso' size='340' side='right' caption='[[5dso]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='5dso' size='340' side='right'caption='[[5dso]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dso]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DSO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DSO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dso]] 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=5DSO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DSO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 1.4Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dsr\|5dsr]]~~, [[~~5dsq~~\|~~5dsq]], [[5dsp\|5dsp]], [[5dsn\|5dsn]], [[5dsm\|5dsm]], [[5dsl\|5dsl]], [[5dsk\|5dsk]], [[5dsj\|5dsj]], [[5dsi\|5dsi~~]]</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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN])</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=5dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dso OCA], [https://pdbe.org/5dso PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dso RCSB], [https://www.ebi.ac.uk/pdbsum/5dso PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dso ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dso OCA], [~~http~~://pdbe.org/5dso PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dso RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dso PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dso ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[~~http~~://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 ==
-	[~~[http~~://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 25:		Line 23:

	==See Also==		==See Also==
-	*[[Carbonic anhydrase\|Carbonic anhydrase]]	+	*[[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: Kim~~, C U~~]]	+	[[Category: Kim CU]]
-	[[Category: McKenna, R]]	+	[[Category: McKenna R]]
-	[[Category: Park~~, S Y]]~~	+	[[Category: Park SY]]
-	~~[[Category: Carbonic anhydrase ii]]~~	+
-	~~[[Category: Co2 release]]~~	+
-	~~[[Category: Intermediate state]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 08:20, 17 October 2018

OCA — Wed, 17 Oct 2018 08:20:58 GMT

←Older revision		Revision as of 08:20, 17 October 2018
Line 3:		Line 3:
	<StructureSection load='5dso' size='340' side='right' caption='[[5dso]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5dso' size='340' side='right' caption='[[5dso]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dso]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DSO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DSO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dso]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DSO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DSO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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">[[5dsr\|5dsr]], [[5dsq\|5dsq]], [[5dsp\|5dsp]], [[5dsn\|5dsn]], [[5dsm\|5dsm]], [[5dsl\|5dsl]], [[5dsk\|5dsk]], [[5dsj\|5dsj]], [[5dsi\|5dsi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dsr\|5dsr]], [[5dsq\|5dsq]], [[5dsp\|5dsp]], [[5dsn\|5dsn]], [[5dsm\|5dsm]], [[5dsl\|5dsl]], [[5dsk\|5dsk]], [[5dsj\|5dsj]], [[5dsi\|5dsi]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CA2 ([http://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'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dso OCA], [http://pdbe.org/5dso PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dso RCSB], [http://www.ebi.ac.uk/pdbsum/5dso PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dso OCA], [http://pdbe.org/5dso PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dso RCSB], [http://www.ebi.ac.uk/pdbsum/5dso PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dso ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 13:		Line 14:
	== Function ==		== Function ==
	[[http://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>		[[http://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 ==
		+	Carbonic anhydrases are mostly zinc metalloenzymes that catalyze the reversible hydration/dehydration of CO2/HCO3 (-) Previously, the X-ray crystal structures of CO2-bound holo (zinc-bound) and apo (zinc-free) human carbonic anhydrase IIs (hCA IIs) were captured at high resolution. Here, we present sequential timeframe structures of holo- [T = 0 s (CO2-bound), 50 s, 3 min, 10 min, 25 min, and 1 h] and apo-hCA IIs [T = 0 s, 50 s, 3 min, and 10 min] during the "slow" release of CO2 Two active site waters, WDW (deep water) and WDW' (this study), replace the vacated space created on CO2 release, and another water, WI (intermediate water), is seen to translocate to the proton wire position W1. In addition, on the rim of the active site pocket, a water W2' (this study), in close proximity to residue His64 and W2, gradually exits the active site, whereas His64 concurrently rotates from pointing away ("out") to pointing toward ("in") active site rotameric conformation. This study provides for the first time, to our knowledge, structural "snapshots" of hCA II intermediate states during the formation of the His64-mediated proton wire that is induced as CO2 is released. Comparison of the holo- and apo-hCA II structures shows that the solvent network rearrangements require the presence of the zinc ion.
		+
		+	Tracking solvent and protein movement during CO2 release in carbonic anhydrase II crystals.,Kim CU, Song H, Avvaru BS, Gruner SM, Park S, McKenna R Proc Natl Acad Sci U S A. 2016 May 10;113(19):5257-62. doi:, 10.1073/pnas.1520786113. Epub 2016 Apr 25. PMID:27114542<ref>PMID:27114542</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5dso" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carbonic anhydrase\|Carbonic anhydrase]]
	== References ==		== References ==
	<references/>		<references/>
Line 18:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Carbonate dehydratase]]		[[Category: Carbonate dehydratase]]
		+	[[Category: Human]]
	[[Category: Kim, C U]]		[[Category: Kim, C U]]
	[[Category: McKenna, R]]		[[Category: McKenna, R]]

OCA at 19:38, 13 May 2016

OCA — Fri, 13 May 2016 19:38:29 GMT

←Older revision		Revision as of 19:38, 13 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5dso is ~~ON HOLD until Paper Publication~~	+	==Structure of CO2 bound apo-form of human carbonic anhydrase II with 0 sec (no) warming==
-		+	<StructureSection load='5dso' size='340' side='right' caption='[[5dso]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors~~: ~~Kim~~, C.U., ~~Park~~, S.Y., ~~McKenna~~, R.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5dso]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DSO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DSO FirstGlance]. <br>
-	~~Description~~: ~~Structure~~ of ~~CO2 bound apo-form of human~~ carbonic anhydrase II with ~~0 sec~~ (no) ~~warming~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dsr\|5dsr]], [[5dsq\|5dsq]], [[5dsp\|5dsp]], [[5dsn\|5dsn]], [[5dsm\|5dsm]], [[5dsl\|5dsl]], [[5dsk\|5dsk]], [[5dsj\|5dsj]], [[5dsi\|5dsi]]</td></tr>
-	[[Category: ~~Park~~, ~~S.Y~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>
-	[[Category: ~~Mckenna~~, R]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dso OCA], [http://pdbe.org/5dso PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dso RCSB], [http://www.ebi.ac.uk/pdbsum/5dso PDBsum]</span></td></tr>
-	[[Category: ~~Kim~~, ~~C.U~~]]	+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[http://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 ==
		+	[[http://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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carbonate dehydratase]]
		+	[[Category: Kim, C U]]
		+	[[Category: McKenna, R]]
		+	[[Category: Park, S Y]]
		+	[[Category: Carbonic anhydrase ii]]
		+	[[Category: Co2 release]]
		+	[[Category: Intermediate state]]
		+	[[Category: Lyase]]

OCA at 11:23, 16 December 2015

OCA — Wed, 16 Dec 2015 11:23:35 GMT

←Older revision		Revision as of 11:23, 16 December 2015
Line 7:		Line 7:
	Description: Structure of CO2 bound apo-form of human carbonic anhydrase II with 0 sec (no) warming		Description: Structure of CO2 bound apo-form of human carbonic anhydrase II with 0 sec (no) warming
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kim, C.U]]
	[[Category: Park, S.Y]]		[[Category: Park, S.Y]]
	[[Category: Mckenna, R]]		[[Category: Mckenna, R]]
		+	[[Category: Kim, C.U]]

OCA: Protected "5dso" [edit=sysop:move=sysop]

OCA — Wed, 30 Sep 2015 13:28:24 GMT

Protected "5dso" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:28, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dso is ON HOLD until Paper Publication Authors: Kim, C.U., Park, S.Y., McKenna, R. Description: Structure of CO2 bound apo-form of human carbonic ...

OCA — Wed, 30 Sep 2015 13:28:23 GMT

New page: '''Unreleased structure''' The entry 5dso is ON HOLD until Paper Publication Authors: Kim, C.U., Park, S.Y., McKenna, R. Description: Structure of CO2 bound apo-form of human carbonic ...

New page

'''Unreleased structure'''

The entry 5dso is ON HOLD until Paper Publication

Authors: Kim, C.U., Park, S.Y., McKenna, R.

Description: Structure of CO2 bound apo-form of human carbonic anhydrase II with 0 sec (no) warming
[[Category: Unreleased Structures]]
[[Category: Kim, C.U]]
[[Category: Park, S.Y]]
[[Category: Mckenna, R]]