6rk9 - Revision history

OCA at 12:22, 24 January 2024

OCA — Wed, 24 Jan 2024 12:22:21 GMT

←Older revision		Revision as of 12:22, 24 January 2024
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	<StructureSection load='6rk9' size='340' side='right'caption='[[6rk9]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='6rk9' size='340' side='right'caption='[[6rk9]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rk9]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5jzz 5jzz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RK9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RK9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rk9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5jzz 5jzz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RK9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MN:MANGANESE+(II)+ION'>MN</scene~~>, ~~<scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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]] 2.292Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jqy\|5jqy]]~~, ~~[[5jz6\|5jz6]], [[5jza\|5jza]], [[5jtc\|5jtc]], [[5jz8\|5jz8]], [[5jzu\|5jzu]], [[5jzz\|5jzz]]~~<~~/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=6rk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rk9 OCA], [https://pdbe.org/6rk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rk9 RCSB], [https://www.ebi.ac.uk/pdbsum/6rk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rk9 ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">ASPH, BAH~~ (~~[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/Peptide-aspartate_beta-dioxygenase Peptide-aspartate beta-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.16 1.14.11.16]~~ </~~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=6rk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rk9 OCA], [~~http~~://pdbe.org/6rk9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rk9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rk9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rk9 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ASPH_HUMAN ASPH_HUMAN]] Isoform 1: specifically hydroxylates an Asp or Asn residue in certain epidermal growth factor-like (EGF) domains of a number of proteins.<ref>PMID:22586105</ref> Isoform 8: membrane-bound Ca(2+)-sensing protein, which is a structural component of the ER-plasma membrane junctions. Isoform 8 regulates the activity of Ca(+2) released-activated Ca(+2) (CRAC) channels in T-cells.<ref>PMID:22586105</ref>	+	[https://www.uniprot.org/uniprot/ASPH_HUMAN ASPH_HUMAN] Isoform 1: specifically hydroxylates an Asp or Asn residue in certain epidermal growth factor-like (EGF) domains of a number of proteins.<ref>PMID:22586105</ref> Isoform 8: membrane-bound Ca(2+)-sensing protein, which is a structural component of the ER-plasma membrane junctions. Isoform 8 regulates the activity of Ca(+2) released-activated Ca(+2) (CRAC) channels in T-cells.<ref>PMID:22586105</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Peptide-aspartate beta-dioxygenase]]~~	+	[[Category: McDonough MA]]
-	[[Category: McDonough~~, M A~~]]	+	[[Category: Pfeffer I]]
-	[[Category: Pfeffer, I]]	+
-	~~[[Category: 2-oxoglutarate dependent oxygenase]]~~	+
-	~~[[Category: Aspartyl/asparaginyl beta-hydroxylase]]~~	+
-	~~[[Category: Double stranded beta-helix]]~~	+
-	~~[[Category: Egf-like domain hydroxylase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Tetratricopeptide repeat~~]]	+

OCA at 08:47, 6 November 2019

OCA — Wed, 06 Nov 2019 08:47:09 GMT

←Older revision		Revision as of 08:47, 6 November 2019
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	<StructureSection load='6rk9' size='340' side='right'caption='[[6rk9]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='6rk9' size='340' side='right'caption='[[6rk9]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rk9]] is a 3 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5jzz 5jzz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RK9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rk9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5jzz 5jzz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RK9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jqy\|5jqy]], [[5jz6\|5jz6]], [[5jza\|5jza]], [[5jtc\|5jtc]], [[5jz8\|5jz8]], [[5jzu\|5jzu]], [[5jzz\|5jzz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jqy\|5jqy]], [[5jz6\|5jz6]], [[5jza\|5jza]], [[5jtc\|5jtc]], [[5jz8\|5jz8]], [[5jzu\|5jzu]], [[5jzz\|5jzz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ASPH, BAH ([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/Peptide-aspartate_beta-dioxygenase Peptide-aspartate beta-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.16 1.14.11.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide-aspartate_beta-dioxygenase Peptide-aspartate beta-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.16 1.14.11.16] </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=6rk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rk9 OCA], [http://pdbe.org/6rk9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rk9 RCSB], [http://www.ebi.ac.uk/pdbsum/6rk9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rk9 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=6rk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rk9 OCA], [http://pdbe.org/6rk9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rk9 RCSB], [http://www.ebi.ac.uk/pdbsum/6rk9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rk9 ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ASPH_HUMAN ASPH_HUMAN]] Isoform 1: specifically hydroxylates an Asp or Asn residue in certain epidermal growth factor-like (EGF) domains of a number of proteins.<ref>PMID:22586105</ref> Isoform 8: membrane-bound Ca(2+)-sensing protein, which is a structural component of the ER-plasma membrane junctions. Isoform 8 regulates the activity of Ca(+2) released-activated Ca(+2) (CRAC) channels in T-cells.<ref>PMID:22586105</ref>		[[http://www.uniprot.org/uniprot/ASPH_HUMAN ASPH_HUMAN]] Isoform 1: specifically hydroxylates an Asp or Asn residue in certain epidermal growth factor-like (EGF) domains of a number of proteins.<ref>PMID:22586105</ref> Isoform 8: membrane-bound Ca(2+)-sensing protein, which is a structural component of the ER-plasma membrane junctions. Isoform 8 regulates the activity of Ca(+2) released-activated Ca(+2) (CRAC) channels in T-cells.<ref>PMID:22586105</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	AspH is an endoplasmic reticulum (ER) membrane-anchored 2-oxoglutarate oxygenase whose C-terminal oxygenase and tetratricopeptide repeat (TPR) domains present in the ER lumen. AspH catalyses hydroxylation of asparaginyl- and aspartyl-residues in epidermal growth factor-like domains (EGFDs). Here we report crystal structures of human AspH, with and without substrate, that reveal substantial conformational changes of the oxygenase and TPR domains during substrate binding. Fe(II)-binding by AspH is unusual, employing only two Fe(II)-binding ligands (His679/His725). Most EGFD structures adopt an established fold with a conserved Cys1-3, 2-4, 5-6 disulfide bonding pattern; an unexpected Cys3-4 disulfide bonding pattern is observed in AspH-EGFD substrate complexes, the catalytic relevance of which is supported by studies involving stable cyclic peptide substrate analogues and by effects of Ca(II) ions on activity. The results have implications for EGFD disulfide pattern processing in the ER and will enable medicinal chemistry efforts targeting human 2OG oxygenases.
		+
		+	Aspartate/asparagine-beta-hydroxylase crystal structures reveal an unexpected epidermal growth factor-like domain substrate disulfide pattern.,Pfeffer I, Brewitz L, Krojer T, Jensen SA, Kochan GT, Kershaw NJ, Hewitson KS, McNeill LA, Kramer H, Munzel M, Hopkinson RJ, Oppermann U, Handford PA, McDonough MA, Schofield CJ Nat Commun. 2019 Oct 28;10(1):4910. doi: 10.1038/s41467-019-12711-7. PMID:31659163<ref>PMID:31659163</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6rk9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Hydroxylases 3D structures\|Hydroxylases 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Peptide-aspartate beta-dioxygenase]]		[[Category: Peptide-aspartate beta-dioxygenase]]

OCA: Protected "6rk9" [edit=sysop:move=sysop]

OCA — Fri, 10 May 2019 11:09:06 GMT

Protected "6rk9" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:09, 10 May 2019

OCA: New page: ==Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and cyclic peptide substrate mimic of factor X==
OCA — Fri, 10 May 2019 11:09:04 GMT

New page: ==Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and cyclic peptide substrate mimic of factor X== <StructureSection load=...

New page

==Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and cyclic peptide substrate mimic of factor X==
<StructureSection load='6rk9' size='340' side='right'caption='[[6rk9]], [[Resolution|resolution]] 2.29Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6rk9]] is a 3 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5jzz 5jzz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RK9 OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RK9 FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl">[[Non-Standard_Residue|NonStd Res:]]</td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[5jqy|5jqy]], [[5jz6|5jz6]], [[5jza|5jza]], [[5jtc|5jtc]], [[5jz8|5jz8]], [[5jzu|5jzu]], [[5jzz|5jzz]]</td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/Peptide-aspartate_beta-dioxygenase Peptide-aspartate beta-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.16 1.14.11.16] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6rk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rk9 OCA], [http://pdbe.org/6rk9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rk9 RCSB], [http://www.ebi.ac.uk/pdbsum/6rk9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rk9 ProSAT]</td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/ASPH_HUMAN ASPH_HUMAN]] Isoform 1: specifically hydroxylates an Asp or Asn residue in certain epidermal growth factor-like (EGF) domains of a number of proteins.<ref>PMID:22586105</ref> Isoform 8: membrane-bound Ca(2+)-sensing protein, which is a structural component of the ER-plasma membrane junctions. Isoform 8 regulates the activity of Ca(+2) released-activated Ca(+2) (CRAC) channels in T-cells.<ref>PMID:22586105</ref>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Large Structures]]
[[Category: Peptide-aspartate beta-dioxygenase]]
[[Category: McDonough, M A]]
[[Category: Pfeffer, I]]
[[Category: 2-oxoglutarate dependent oxygenase]]
[[Category: Aspartyl/asparaginyl beta-hydroxylase]]
[[Category: Double stranded beta-helix]]
[[Category: Egf-like domain hydroxylase]]
[[Category: Oxidoreductase]]
[[Category: Tetratricopeptide repeat]]