5v7y - Revision history

OCA at 13:43, 4 October 2023

2023-10-04T13:43:35Z

←Older revision		Revision as of 13:43, 4 October 2023
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	<StructureSection load='5v7y' size='340' side='right'caption='[[5v7y]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5v7y' size='340' side='right'caption='[[5v7y]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v7y]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var.~~ anthracis~~" (cohn 1872) smith et al. 1946~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V7Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v7y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V7Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=TFA:TRIFLUOROACETIC+ACID'>TFA</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]] 2.05Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BASH2_01493, BVB96_22550 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=TFA:TRIFLUOROACETIC+ACID'>TFA</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=5v7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7y OCA], [~~http~~://pdbe.org/5v7y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v7y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v7y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7y 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=5v7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7y OCA], [https://pdbe.org/5v7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v7y RCSB], [https://www.ebi.ac.uk/pdbsum/5v7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7y ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A4Y1WAP5_BACAN A0A4Y1WAP5_BACAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5v7y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5v7y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
		+	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus anthracis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dey, M]]	+	[[Category: Dey M]]
-	[[Category: Schnicker~~, N J]]~~	+	[[Category: Schnicker NJ]]
-	~~[[Category: Cupin]]~~	+
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Prolyl 4-hydroxylase~~]]	+

OCA at 16:54, 20 November 2019

2019-11-20T16:54:00Z

←Older revision		Revision as of 16:54, 20 November 2019
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	==Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu==		==Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu==
-	<StructureSection load='5v7y' size='340' side='right' caption='[[5v7y]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5v7y' size='340' side='right'caption='[[5v7y]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5v7y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[5v7y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7Y FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Dey, M]]		[[Category: Dey, M]]
	[[Category: Schnicker, N J]]		[[Category: Schnicker, N J]]

OCA at 10:23, 8 November 2017

2017-11-08T10:23:25Z

←Older revision		Revision as of 10:23, 8 November 2017
Line 3:		Line 3:
	<StructureSection load='5v7y' size='340' side='right' caption='[[5v7y]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5v7y' size='340' side='right' caption='[[5v7y]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v7y]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v7y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=TFA:TRIFLUOROACETIC+ACID'>TFA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=TFA:TRIFLUOROACETIC+ACID'>TFA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BASH2_01493, BVB96_22550 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</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=5v7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7y OCA], [http://pdbe.org/5v7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7y RCSB], [http://www.ebi.ac.uk/pdbsum/5v7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7y 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=5v7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7y OCA], [http://pdbe.org/5v7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7y RCSB], [http://www.ebi.ac.uk/pdbsum/5v7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7y ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:58, 18 October 2017

2017-10-18T06:58:58Z

←Older revision		Revision as of 06:58, 18 October 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5v7y is ~~ON HOLD until Paper~~ Publication	+	==Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu==
		+	<StructureSection load='5v7y' size='340' side='right' caption='[[5v7y]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5v7y]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7Y FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=TFA:TRIFLUOROACETIC+ACID'>TFA</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=5v7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7y OCA], [http://pdbe.org/5v7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7y RCSB], [http://www.ebi.ac.uk/pdbsum/5v7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7y ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Prolyl hydroxylation is a very common post-translational modification and has many roles in eukaryotes such as, collagen stabilization, hypoxia sensing, and controlling protein transcription and translation. There is growing evidence suggesting prokaryotes contain prolyl 4-hydroxylases (P4Hs) homologous to the hypoxia-inducible factor (HIF)-prolyl hydroxylase domains (PHDs) that act on elongation factor Tu (EFTu) and are likely involved in the regulation of bacterial translation. Recent biochemical and structural studies with a PHD from Pseudomonas putida (PPHD) determined that it forms a complex with EFTu and hydroxylates a prolyl residue of EFTu. Moreover, while animal, plant, and viral P4Hs act on peptidyl proline, most prokaryotic P4Hs have been known to target free L-proline; the exceptions include PPHD and a P4H from Bacillus anthracis (BaP4H) that modifies collagen-like proline-rich peptides. Here we use biophysical and mass spectrometric methods to demonstrate that BaP4H recognizes full-length BaEFTu and a BaEFTu 9-mer peptide for site-specific proline hydroxylation. Using size-exclusion chromatography-small angle X-ray scattering (SEC-SAXS) and binding studies we identified that BaP4H forms a 1:1 heterodimeric complex with BaEFTu. The SEC-SAXS studies reveal dissociation of BaP4H dimeric subunits upon interaction with BaEFTu. While BaP4H is unusual within bacteria in that it is structurally and functionally similar to the animal PHDs and collagen P4Hs respectively, this work further provides evidence for its promiscuous substrate recognition. It is possible that the enzyme might have evolved to hydroxylate a universally conserved protein in prokaryotes, similar to the PHDs and implies a functional role in B. anthracis.

-	~~Authors~~:	+	Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu.,Schnicker NJ, Razzaghi M, Guha Thakurta S, Chakravarthy S, Dey M Biochemistry. 2017 Oct 5. doi: 10.1021/acs.biochem.7b00601. PMID:28981257<ref>PMID:28981257</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5v7y" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dey, M]]
		+	[[Category: Schnicker, N J]]
		+	[[Category: Cupin]]
		+	[[Category: Dioxygenase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Prolyl 4-hydroxylase]]

OCA at 09:42, 12 April 2017

2017-04-12T09:42:43Z

←Older revision		Revision as of 09:42, 12 April 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5v7y is ON HOLD	+	The entry 5v7y is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5v7y" [edit=sysop:move=sysop]

2017-04-05T11:42:37Z

Protected "5v7y" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:42, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v7y is ON HOLD Authors: Description: Category: Unreleased Structures

2017-04-05T11:42:36Z

New page: '''Unreleased structure''' The entry 5v7y is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5v7y is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]