2vhb - Revision history

OCA at 09:24, 21 February 2024

2024-02-21T09:24:45Z

←Older revision		Revision as of 09:24, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2vhb' size='340' side='right'caption='[[2vhb]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='2vhb' size='340' side='right'caption='[[2vhb]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vhb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_15218 Atcc 15218~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vhb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vitreoscilla_stercoraria Vitreoscilla stercoraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VHB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>~~, ~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.76Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~VGB ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=61 ATCC 15218])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=2vhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhb OCA], [https://pdbe.org/2vhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vhb RCSB], [https://www.ebi.ac.uk/pdbsum/2vhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vhb 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=2vhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhb OCA], [https://pdbe.org/2vhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vhb RCSB], [https://www.ebi.ac.uk/pdbsum/2vhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vhb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BAHG_VITST BAHG_VITST]] This protein functions as a terminal oxidase.	+	[https://www.uniprot.org/uniprot/BAHG_VITST BAHG_VITST] This protein functions as a terminal oxidase.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vhb ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vhb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: The first hemoglobin identified in bacteria was isolated from Vitreoscilla stercoraria (VtHb) as a homodimeric species. The wild-type protein has been reported to display medium oxygen affinity and cooperative ligand-binding properties. Moreover, VtHb can support aerobic growth in Escherichia coli with impaired terminal oxidase function. This ability of VtHb to improve the growth properties of E. coli has important applications in fermentation technology, assisting the overexpression of recombinant proteins and antibiotics. Oxygen binding heme domains have been identified in chimeric proteins from bacteria and yeast, where they are covalently linked to FAD- and NAD(P)H-binding domains. We investigate here the fold, the distal heme site structure and the quaternary assembly of a bacterial hemoglobin which does not bear the typical flavohemoglobin domain organization. RESULTS: The VtHb three-dimensional structure conforms to the well known globin fold. Nevertheless, the polypeptide segment connecting helices C and E is disordered, and residues E7-E10 (defined according to the standard globin fold nomenclature) do not adopt the usual alpha-helical conformation, thus locating Gln53(E7) out of the heme pocket. Binding of azide to the heme iron introduces substantial structural perturbations in the heme distal site residues, particularly Tyr29(B10) and Pro54(E8). The quaternary assembly of homodimeric VtHb, not observed before within the globin family, is based on a molecular interface defined by helices F and H of both subunits, the two heme iron atoms being 34 A apart. CONCLUSIONS: The unusual heme distal site structure observed shows that previously undescribed molecular mechanisms of ligand stabilization are operative in VtHb. The polypeptide chain disorder observed in the CE region indicates a potential site of interaction with the FAD/NADH reductase partner, in analogy with observations in the chimeric flavohemoglobin from Alcaligenes eutrophus.
-
-	Unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from Vitreoscilla sp.,Tarricone C, Galizzi A, Coda A, Ascenzi P, Bolognesi M Structure. 1997 Apr 15;5(4):497-507. PMID:9115439<ref>PMID:9115439</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2vhb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Hemoglobin 3D structures\|Hemoglobin 3D structures]]		*[[Hemoglobin 3D structures\|Hemoglobin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 15218]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ascenzi, P]]	+	[[Category: Vitreoscilla stercoraria]]
-	[[Category: Bolognesi, M]]	+	[[Category: Ascenzi P]]
-	[[Category: Coda, A]]	+	[[Category: Bolognesi M]]
-	[[Category: Galizzi, A]]	+	[[Category: Coda A]]
-	[[Category: Tarricone, C]]	+	[[Category: Galizzi A]]
-	~~[[Category: Heme]]~~	+	[[Category: Tarricone C]]
-	~~[[Category: Oxygen transport]]~~	+
-	~~[[Category: Respiratory protein~~]]	+

OCA at 10:45, 7 July 2021

2021-07-07T10:45:24Z

←Older revision		Revision as of 10:45, 7 July 2021
Line 1:		Line 1:

	==AZIDE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA STERCORARIA==		==AZIDE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA STERCORARIA==
-	<StructureSection load='2vhb' size='340' side='right' caption='[[2vhb]], [[Resolution\|resolution]] 1.76Å' scene=''>	+	<StructureSection load='2vhb' size='340' side='right'caption='[[2vhb]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vhb]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_15218 Atcc 15218]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2VHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vhb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_15218 Atcc 15218]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VHB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VGB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=61 ATCC 15218])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VGB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=61 ATCC 15218])</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=2vhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhb OCA], [~~http~~://pdbe.org/2vhb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2vhb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2vhb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2vhb 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=2vhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhb OCA], [https://pdbe.org/2vhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vhb RCSB], [https://www.ebi.ac.uk/pdbsum/2vhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vhb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BAHG_VITST BAHG_VITST]] This protein functions as a terminal oxidase.	+	[[https://www.uniprot.org/uniprot/BAHG_VITST BAHG_VITST]] This protein functions as a terminal oxidase.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 15218]]		[[Category: Atcc 15218]]
		+	[[Category: Large Structures]]
	[[Category: Ascenzi, P]]		[[Category: Ascenzi, P]]
	[[Category: Bolognesi, M]]		[[Category: Bolognesi, M]]

OCA at 21:29, 19 September 2018

2018-09-19T21:29:05Z

←Older revision		Revision as of 21:29, 19 September 2018
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vh/2vhb_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vh/2vhb_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 22:11, 5 August 2016

2016-08-05T22:11:55Z

←Older revision		Revision as of 22:11, 5 August 2016
Line 1:		Line 1:
		+
	==AZIDE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA STERCORARIA==		==AZIDE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA STERCORARIA==
	<StructureSection load='2vhb' size='340' side='right' caption='[[2vhb]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='2vhb' size='340' side='right' caption='[[2vhb]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vhb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Vitreoscilla_stercoraria Vitreoscilla stercoraria~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vhb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_15218 Atcc 15218]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VHB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VGB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=61 ~~Vitreoscilla stercoraria~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VGB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=61 ATCC 15218])</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=2vhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vhb RCSB], [http://www.ebi.ac.uk/pdbsum/2vhb 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=2vhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhb OCA], [http://pdbe.org/2vhb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vhb RCSB], [http://www.ebi.ac.uk/pdbsum/2vhb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vhb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vhb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2vhb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vitreoscilla stercoraria~~]]	+	[[Category: Atcc 15218]]
	[[Category: Ascenzi, P]]		[[Category: Ascenzi, P]]
	[[Category: Bolognesi, M]]		[[Category: Bolognesi, M]]

OCA at 22:21, 25 December 2014

2014-12-25T22:21:52Z

←Older revision		Revision as of 22:21, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vhb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vitreoscilla_stercoraria Vitreoscilla stercoraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VHB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vhb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vitreoscilla_stercoraria Vitreoscilla stercoraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VHB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VGB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=61 Vitreoscilla stercoraria])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VGB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=61 Vitreoscilla stercoraria])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vhb RCSB], [http://www.ebi.ac.uk/pdbsum/2vhb 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=2vhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vhb RCSB], [http://www.ebi.ac.uk/pdbsum/2vhb PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BAHG_VITST BAHG_VITST]] This protein functions as a terminal oxidase.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Vitreoscilla stercoraria]]		[[Category: Vitreoscilla stercoraria]]
-	[[Category: Ascenzi, P.]]	+	[[Category: Ascenzi, P]]
-	[[Category: Bolognesi, M.]]	+	[[Category: Bolognesi, M]]
-	[[Category: Coda, A.]]	+	[[Category: Coda, A]]
-	[[Category: Galizzi, A.]]	+	[[Category: Galizzi, A]]
-	[[Category: Tarricone, C.]]	+	[[Category: Tarricone, C]]
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Oxygen transport]]		[[Category: Oxygen transport]]
	[[Category: Respiratory protein]]		[[Category: Respiratory protein]]

OCA at 09:25, 29 September 2014

2014-09-29T09:25:07Z

←Older revision		Revision as of 09:25, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2vhb.~~png~~\|~~left~~\|200px]]	+	==AZIDE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA STERCORARIA==
		+	<StructureSection load='2vhb' size='340' side='right' caption='[[2vhb]], [[Resolution\|resolution]] 1.76Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2vhb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vitreoscilla_stercoraria Vitreoscilla stercoraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VHB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VGB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=61 Vitreoscilla stercoraria])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vhb RCSB], [http://www.ebi.ac.uk/pdbsum/2vhb PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vh/2vhb_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: The first hemoglobin identified in bacteria was isolated from Vitreoscilla stercoraria (VtHb) as a homodimeric species. The wild-type protein has been reported to display medium oxygen affinity and cooperative ligand-binding properties. Moreover, VtHb can support aerobic growth in Escherichia coli with impaired terminal oxidase function. This ability of VtHb to improve the growth properties of E. coli has important applications in fermentation technology, assisting the overexpression of recombinant proteins and antibiotics. Oxygen binding heme domains have been identified in chimeric proteins from bacteria and yeast, where they are covalently linked to FAD- and NAD(P)H-binding domains. We investigate here the fold, the distal heme site structure and the quaternary assembly of a bacterial hemoglobin which does not bear the typical flavohemoglobin domain organization. RESULTS: The VtHb three-dimensional structure conforms to the well known globin fold. Nevertheless, the polypeptide segment connecting helices C and E is disordered, and residues E7-E10 (defined according to the standard globin fold nomenclature) do not adopt the usual alpha-helical conformation, thus locating Gln53(E7) out of the heme pocket. Binding of azide to the heme iron introduces substantial structural perturbations in the heme distal site residues, particularly Tyr29(B10) and Pro54(E8). The quaternary assembly of homodimeric VtHb, not observed before within the globin family, is based on a molecular interface defined by helices F and H of both subunits, the two heme iron atoms being 34 A apart. CONCLUSIONS: The unusual heme distal site structure observed shows that previously undescribed molecular mechanisms of ligand stabilization are operative in VtHb. The polypeptide chain disorder observed in the CE region indicates a potential site of interaction with the FAD/NADH reductase partner, in analogy with observations in the chimeric flavohemoglobin from Alcaligenes eutrophus.

-	~~{{STRUCTURE_2vhb\| PDB=2vhb \| SCENE= }}~~	+	Unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from Vitreoscilla sp.,Tarricone C, Galizzi A, Coda A, Ascenzi P, Bolognesi M Structure. 1997 Apr 15;5(4):497-507. PMID:9115439<ref>PMID:9115439</ref>

-	~~===AZIDE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA STERCORARIA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9115439}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2vhb]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Vitreoscilla_stercoraria Vitreoscilla stercoraria]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA].~~	+

	==See Also==		==See Also==
-	*[[Hemoglobin\|Hemoglobin]]	+	*[[Hemoglobin 3D structures\|Hemoglobin 3D structures]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009115439<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Vitreoscilla stercoraria]]		[[Category: Vitreoscilla stercoraria]]
	[[Category: Ascenzi, P.]]		[[Category: Ascenzi, P.]]

OCA at 22:20, 20 October 2012

2012-10-20T22:20:32Z

←Older revision		Revision as of 22:20, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2vhb]] is a 2 chain structure ~~of [[Hemoglobin]]~~ with sequence from [http://en.wikipedia.org/wiki/Vitreoscilla_stercoraria Vitreoscilla stercoraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA].	+	[[2vhb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vitreoscilla_stercoraria Vitreoscilla stercoraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA].

	==See Also==		==See Also==

OCA: Protected "2vhb" [edit=sysop:move=sysop]

2012-07-27T15:59:20Z

Protected "2vhb" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:59, 27 July 2012

OCA at 15:59, 27 July 2012

2012-07-27T15:59:18Z

←Older revision		Revision as of 15:59, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2vhb.png\|left\|200px]]		[[Image:2vhb.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2vhb", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
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	{{STRUCTURE_2vhb\| PDB=2vhb \| SCENE= }}		{{STRUCTURE_2vhb\| PDB=2vhb \| SCENE= }}

	===AZIDE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA STERCORARIA===		===AZIDE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA STERCORARIA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9115439}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9115439 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9115439}}		{{ABSTRACT_PUBMED_9115439}}

	==About this Structure==		==About this Structure==
-	~~2VHB~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Vitreoscilla_stercoraria Vitreoscilla stercoraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA].	+	[[2vhb]] is a 2 chain structure of [[Hemoglobin]] with sequence from [http://en.wikipedia.org/wiki/Vitreoscilla_stercoraria Vitreoscilla stercoraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA].
		+
		+	==See Also==
		+	*[[Hemoglobin\|Hemoglobin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9115439~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009115439</ref><references group="xtra"/>
	[[Category: Vitreoscilla stercoraria]]		[[Category: Vitreoscilla stercoraria]]
	[[Category: Ascenzi, P.]]		[[Category: Ascenzi, P.]]
Line 33:		Line 24:
	[[Category: Oxygen transport]]		[[Category: Oxygen transport]]
	[[Category: Respiratory protein]]		[[Category: Respiratory protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:37:27 2009''

OCA at 07:37, 18 February 2009

2009-02-18T07:37:29Z

←Older revision		Revision as of 07:37, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2VHB is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Vitreoscilla_stercoraria Vitreoscilla stercoraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA].	+	2VHB is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Vitreoscilla_stercoraria Vitreoscilla stercoraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHB OCA].

	==Reference==		==Reference==
-	~~Unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from Vitreoscilla sp., Tarricone C, Galizzi A, Coda A, Ascenzi P, Bolognesi M, Structure. 1997 Apr 15;5(4):497-507.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9115439 9115439]~~	+	<ref group="xtra">PMID:9115439</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Vitreoscilla stercoraria]]		[[Category: Vitreoscilla stercoraria]]
	[[Category: Ascenzi, P.]]		[[Category: Ascenzi, P.]]
Line 35:		Line 34:
	[[Category: Respiratory protein]]		[[Category: Respiratory protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 15~~:54:~~29 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:37:27 2009''