5ziq - Revision history

OCA at 10:27, 27 March 2024

OCA — Wed, 27 Mar 2024 10:27:58 GMT

←Older revision		Revision as of 10:27, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5ziq' size='340' side='right'caption='[[5ziq]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5ziq' size='340' side='right'caption='[[5ziq]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ziq]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ramva Ramva~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZIQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZIQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ziq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ramazzottius_varieornatus Ramazzottius varieornatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZIQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.5Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RvY_09119-1, RvY_09119.1, RvY_09119 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=947166 RAMVA])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5ziq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ziq OCA], [~~http~~://pdbe.org/5ziq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ziq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ziq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ziq 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=5ziq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ziq OCA], [https://pdbe.org/5ziq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ziq RCSB], [https://www.ebi.ac.uk/pdbsum/5ziq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ziq ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A1D1V896_RAMVA A0A1D1V896_RAMVA]
-	Tardigrades, also known as water bears, can survive extreme conditions. For example, tardigrades have high tolerance to extreme desiccation because they can enter an anhydrobiotic state, in which they show no or nearly undetectable metabolic processes. Proteins from anhydrobiotic tardigrades with low homology to known proteins from other organisms are new potential targets for structural genomics. Here, we present spectroscopic and structural characterization of an unprecedented globin protein (Kumaglobin: Kgb) found in an anhydrobiotic tardigrade. Spectroscopy reveals that Kgb contains hexacoordinated low-spin heme, which is not capable of binding to hydrogen sulfide (H2 S) unlike other globin proteins, such as neuroglobin. Interestingly however, when distal histidine is replaced with alanine, H2 S is capable of binding to heme, implying that the distal histidine of Kgb binds tightly to heme. The overall structure of Kgb at 1.5 A resolution shows high resemblance to well-characterized eukaryotic globin proteins, such as myoglobin and cytoglobin. However, the heme coordination geometry in Kgb is unique because the distal histidinyl ligand is located at the 11th position of helix E while it is found at 7th position on helix E in many known globin proteins. The unusual conformation of distal histidine in Kgb is stabilized by a hydrogen bond with the carbonyl O atom of A103. Furthermore, bulky residues exist around the heme cofactor, resulting in a ruffling conformation of the porphyrin ring. Based on our study, Kgb is thought to be involved in electron transfer or enzymatic reactions rather than transporting or storing ligands. DATABASE: Structural data are available in the Protein Data Bank under the accession numbers 5ZIQ (Kgb4-SR) and 5ZM9 (Kgb7-house).	+
-		+
-	~~Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus.,Kim J, Fukuda Y, Inoue T FEBS J. 2018 Dec 1. doi: 10.1111~~/~~febs.14713. PMID:30506636<ref>PMID:30506636<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5ziq" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ramva~~]]	+	[[Category: Ramazzottius varieornatus]]
-	[[Category: Fukuda, Y]]	+	[[Category: Fukuda Y]]
-	[[Category: Inoue, T]]	+	[[Category: Inoue T]]
-	[[Category: Kim, J]]	+	[[Category: Kim J]]
-	~~[[Category: Globin]]~~	+
-	~~[[Category: Oxygen transport]]~~	+
-	~~[[Category: Tardigrade]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 07:43, 24 April 2019

OCA — Wed, 24 Apr 2019 07:43:37 GMT

←Older revision		Revision as of 07:43, 24 April 2019
Line 1:		Line 1:

	==Crystal structure of hexacoordinated heme protein from anhydrobiotic tardigrade at pH 4==		==Crystal structure of hexacoordinated heme protein from anhydrobiotic tardigrade at pH 4==
-	<StructureSection load='5ziq' size='340' side='right' caption='[[5ziq]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='5ziq' size='340' side='right'caption='[[5ziq]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ziq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZIQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZIQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ziq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ramva Ramva]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZIQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZIQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RvY_09119-1, RvY_09119.1, RvY_09119 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=947166 RAMVA])</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=5ziq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ziq OCA], [http://pdbe.org/5ziq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ziq RCSB], [http://www.ebi.ac.uk/pdbsum/5ziq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ziq ProSAT]</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=5ziq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ziq OCA], [http://pdbe.org/5ziq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ziq RCSB], [http://www.ebi.ac.uk/pdbsum/5ziq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ziq ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ramva]]
	[[Category: Fukuda, Y]]		[[Category: Fukuda, Y]]
	[[Category: Inoue, T]]		[[Category: Inoue, T]]

OCA at 06:08, 2 January 2019

OCA — Wed, 02 Jan 2019 06:08:15 GMT

←Older revision		Revision as of 06:08, 2 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ziq is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of hexacoordinated heme protein from anhydrobiotic tardigrade at pH 4==
		+	<StructureSection load='5ziq' size='340' side='right' caption='[[5ziq]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ziq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZIQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZIQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5ziq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ziq OCA], [http://pdbe.org/5ziq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ziq RCSB], [http://www.ebi.ac.uk/pdbsum/5ziq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ziq ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tardigrades, also known as water bears, can survive extreme conditions. For example, tardigrades have high tolerance to extreme desiccation because they can enter an anhydrobiotic state, in which they show no or nearly undetectable metabolic processes. Proteins from anhydrobiotic tardigrades with low homology to known proteins from other organisms are new potential targets for structural genomics. Here, we present spectroscopic and structural characterization of an unprecedented globin protein (Kumaglobin: Kgb) found in an anhydrobiotic tardigrade. Spectroscopy reveals that Kgb contains hexacoordinated low-spin heme, which is not capable of binding to hydrogen sulfide (H2 S) unlike other globin proteins, such as neuroglobin. Interestingly however, when distal histidine is replaced with alanine, H2 S is capable of binding to heme, implying that the distal histidine of Kgb binds tightly to heme. The overall structure of Kgb at 1.5 A resolution shows high resemblance to well-characterized eukaryotic globin proteins, such as myoglobin and cytoglobin. However, the heme coordination geometry in Kgb is unique because the distal histidinyl ligand is located at the 11th position of helix E while it is found at 7th position on helix E in many known globin proteins. The unusual conformation of distal histidine in Kgb is stabilized by a hydrogen bond with the carbonyl O atom of A103. Furthermore, bulky residues exist around the heme cofactor, resulting in a ruffling conformation of the porphyrin ring. Based on our study, Kgb is thought to be involved in electron transfer or enzymatic reactions rather than transporting or storing ligands. DATABASE: Structural data are available in the Protein Data Bank under the accession numbers 5ZIQ (Kgb4-SR) and 5ZM9 (Kgb7-house).

-	~~Authors~~: ~~Kim~~, J., ~~Fukuda~~, Y., Inoue, T.	+	Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus.,Kim J, Fukuda Y, Inoue T FEBS J. 2018 Dec 1. doi: 10.1111/febs.14713. PMID:30506636<ref>PMID:30506636</ref>

-	~~Description: Crystal structure~~ of ~~hexacoordinated heme protein from anhydrobiotic tardigrade at pH 4~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Inoue, T]]~~	+	<div class="pdbe-citations 5ziq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Fukuda, Y]]		[[Category: Fukuda, Y]]
		+	[[Category: Inoue, T]]
	[[Category: Kim, J]]		[[Category: Kim, J]]
		+	[[Category: Globin]]
		+	[[Category: Oxygen transport]]
		+	[[Category: Tardigrade]]
		+	[[Category: Unknown function]]

OCA at 05:46, 23 May 2018

OCA — Wed, 23 May 2018 05:46:31 GMT

←Older revision		Revision as of 05:46, 23 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ziq is ON HOLD	+	The entry 5ziq is ON HOLD until Paper Publication

	Authors: Kim, J., Fukuda, Y., Inoue, T.		Authors: Kim, J., Fukuda, Y., Inoue, T.

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

OCA — Wed, 21 Mar 2018 06:04:38 GMT

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

←Older revision

Revision as of 06:04, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 5ziq is ON HOLD Authors: Kim, J., Fukuda, Y., Inoue, T. Description: Crystal structure of hexacoordinated heme protein from anhydrobiotic tardigrad...

OCA — Wed, 21 Mar 2018 06:04:37 GMT

New page: '''Unreleased structure''' The entry 5ziq is ON HOLD Authors: Kim, J., Fukuda, Y., Inoue, T. Description: Crystal structure of hexacoordinated heme protein from anhydrobiotic tardigrad...

New page

'''Unreleased structure'''

The entry 5ziq is ON HOLD

Authors: Kim, J., Fukuda, Y., Inoue, T.

Description: Crystal structure of hexacoordinated heme protein from anhydrobiotic tardigrade at pH 4
[[Category: Unreleased Structures]]
[[Category: Inoue, T]]
[[Category: Fukuda, Y]]
[[Category: Kim, J]]