5lzl - Revision history

OCA at 18:18, 1 November 2023

OCA — Wed, 01 Nov 2023 18:18:17 GMT

←Older revision		Revision as of 18:18, 1 November 2023
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	<StructureSection load='5lzl' size='340' side='right'caption='[[5lzl]], [[Resolution\|resolution]] 3.47Å' scene=''>		<StructureSection load='5lzl' size='340' side='right'caption='[[5lzl]], [[Resolution\|resolution]] 3.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lzl]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrcj Pyrcj~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LZL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LZL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lzl]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_calidifontis_JCM_11548 Pyrobaculum calidifontis JCM 11548]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LZL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LZL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.47Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">Pcal_1709 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=410359 PYRCJ])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Porphobilinogen_synthase Porphobilinogen synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.24 4.2.1.24]~~ </~~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=5lzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lzl OCA], [https://pdbe.org/5lzl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lzl RCSB], [https://www.ebi.ac.uk/pdbsum/5lzl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lzl 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=5lzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lzl OCA], [~~http~~://pdbe.org/5lzl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5lzl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5lzl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5lzl ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A3MWV9_PYRCJ A3MWV9_PYRCJ]
	<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 5lzl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5lzl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Porphobilinogen synthase\|Porphobilinogen synthase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Porphobilinogen synthase]]~~	+	[[Category: Pyrobaculum calidifontis JCM 11548]]
-	~~[[Category: Pyrcj~~]]	+	[[Category: Azim N]]
-	[[Category: Azim, N]]	+	[[Category: Cooper JB]]
-	[[Category: Cooper~~, J B~~]]	+	[[Category: Erskine PT]]
-	[[Category: Erskine~~, P T~~]]	+	[[Category: Guo J]]
-	[[Category: Guo, J]]	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Tetrapyrrole biosynthesis]]~~	+
-	~~[[Category: Tim-barrel~~]]	+

OCA at 06:10, 10 July 2019

OCA — Wed, 10 Jul 2019 06:10:48 GMT

←Older revision		Revision as of 06:10, 10 July 2019
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	==Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase==		==Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase==
-	<StructureSection load='5lzl' size='340' side='right' caption='[[5lzl]], [[Resolution\|resolution]] 3.47Å' scene=''>	+	<StructureSection load='5lzl' size='340' side='right'caption='[[5lzl]], [[Resolution\|resolution]] 3.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5lzl]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrcj Pyrcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LZL FirstGlance]. <br>		<table><tr><td colspan='2'>[[5lzl]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrcj Pyrcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LZL FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Porphobilinogen synthase]]		[[Category: Porphobilinogen synthase]]
	[[Category: Pyrcj]]		[[Category: Pyrcj]]

OCA at 22:02, 9 August 2018

OCA — Thu, 09 Aug 2018 22:02:24 GMT

←Older revision		Revision as of 22:02, 9 August 2018
Line 3:		Line 3:
	<StructureSection load='5lzl' size='340' side='right' caption='[[5lzl]], [[Resolution\|resolution]] 3.47Å' scene=''>		<StructureSection load='5lzl' size='340' side='right' caption='[[5lzl]], [[Resolution\|resolution]] 3.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lzl]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LZL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lzl]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrcj Pyrcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LZL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pcal_1709 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=410359 PYRCJ])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Porphobilinogen_synthase Porphobilinogen synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.24 4.2.1.24] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Porphobilinogen_synthase Porphobilinogen synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.24 4.2.1.24] </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=5lzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lzl OCA], [http://pdbe.org/5lzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lzl RCSB], [http://www.ebi.ac.uk/pdbsum/5lzl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lzl 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=5lzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lzl OCA], [http://pdbe.org/5lzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lzl RCSB], [http://www.ebi.ac.uk/pdbsum/5lzl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lzl ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Porphobilinogen synthase]]		[[Category: Porphobilinogen synthase]]
		+	[[Category: Pyrcj]]
	[[Category: Azim, N]]		[[Category: Azim, N]]
	[[Category: Cooper, J B]]		[[Category: Cooper, J B]]

OCA at 16:35, 25 January 2017

OCA — Wed, 25 Jan 2017 16:35:39 GMT

←Older revision		Revision as of 16:35, 25 January 2017
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	<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=5lzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lzl OCA], [http://pdbe.org/5lzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lzl RCSB], [http://www.ebi.ac.uk/pdbsum/5lzl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lzl 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=5lzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lzl OCA], [http://pdbe.org/5lzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lzl RCSB], [http://www.ebi.ac.uk/pdbsum/5lzl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lzl ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A number of X-ray analyses of an enzyme involved in a key early stage of tetrapyrrole biosynthesis are reported. Two structures of human 5-aminolaevulinate dehydratase (ALAD), native and recombinant, have been determined at 2.8 A resolution, showing that the enzyme adopts an octameric quaternary structure in accord with previously published analyses of the enzyme from a range of other species. However, this is in contrast to the finding that a disease-related F12L mutant of the human enzyme uniquely forms hexamers [Breinig et al. (2003), Nature Struct. Biol. 10, 757-763]. Monomers of all ALADs adopt the TIM-barrel fold; the subunit conformation that assembles into the octamer includes the N-terminal tail of one monomer curled around the (alpha/beta)8 barrel of a neighbouring monomer. Both crystal forms of the human enzyme possess two monomers per asymmetric unit, termed A and B. In the native enzyme there are a number of distinct structural differences between the A and B monomers, with the latter exhibiting greater disorder in a number of loop regions and in the active site. In contrast, the second monomer of the recombinant enzyme appears to be better defined and the active site of both monomers clearly possesses a zinc ion which is bound by three conserved cysteine residues. In native human ALAD, the A monomer also has a ligand resembling the substrate ALA which is covalently bound by a Schiff base to one of the active-site lysines (Lys252) and is held in place by an ordered active-site loop. In contrast, these features of the active-site structure are disordered or absent in the B subunit of the native human enzyme. The octameric structure of the zinc-dependent ALAD from the hyperthermophile Pyrobaculum calidifontis is also reported at a somewhat lower resolution of 3.5 A. Finally, the details are presented of a high-resolution structure of the Escherichia coli ALAD enzyme co-crystallized with a noncovalently bound moiety of the product, porphobilinogen (PBG). This structure reveals that the pyrrole side-chain amino group is datively bound to the active-site zinc ion and that the PBG carboxylates interact with the enzyme via hydrogen bonds and salt bridges with invariant residues. A number of hydrogen-bond interactions that were previously observed in the structure of yeast ALAD with a cyclic intermediate resembling the product PBG appear to be weaker in the new structure, suggesting that these interactions are only optimal in the transition state.
		+
		+	Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans, Escherichia coli and the hyperthermophile Pyrobaculum calidifontis.,Mills-Davies N, Butler D, Norton E, Thompson D, Sarwar M, Guo J, Gill R, Azim N, Coker A, Wood SP, Erskine PT, Coates L, Cooper JB, Rashid N, Akhtar M, Shoolingin-Jordan PM Acta Crystallogr D Struct Biol. 2017 Jan 1;73(Pt 1):9-21. doi:, 10.1107/S2059798316019525. Epub 2017 Jan 1. PMID:28045381<ref>PMID:28045381</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5lzl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:45, 19 October 2016

OCA — Wed, 19 Oct 2016 17:45:49 GMT

←Older revision		Revision as of 17:45, 19 October 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5lzl is ~~ON HOLD~~	+	==Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase==
-		+	<StructureSection load='5lzl' size='340' side='right' caption='[[5lzl]], [[Resolution\|resolution]] 3.47Å' scene=''>
-	~~Authors~~: ~~Azim~~, N., ~~Erskine, P~~.T., ~~Guo~~, J., ~~Cooper~~, J.B.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5lzl]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LZL FirstGlance]. <br>
-	~~Description~~: ~~Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Porphobilinogen_synthase Porphobilinogen synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.24 4.2.1.24] </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=5lzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lzl OCA], [http://pdbe.org/5lzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lzl RCSB], [http://www.ebi.ac.uk/pdbsum/5lzl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lzl ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Porphobilinogen synthase]]
		+	[[Category: Azim, N]]
		+	[[Category: Cooper, J B]]
		+	[[Category: Erskine, P T]]
	[[Category: Guo, J]]		[[Category: Guo, J]]
-	[[Category: ~~Erskine, P.T~~]]	+	[[Category: Lyase]]
-	[[Category: ~~Azim, N~~]]	+	[[Category: Tetrapyrrole biosynthesis]]
-	[[Category: ~~Cooper, J.B~~]]	+	[[Category: Tim-barrel]]

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

OCA — Wed, 05 Oct 2016 19:24:49 GMT

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

←Older revision

Revision as of 19:24, 5 October 2016

OCA: New page: '''Unreleased structure''' The entry 5lzl is ON HOLD Authors: Azim, N., Erskine, P.T., Guo, J., Cooper, J.B. Description: Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase [[...

OCA — Wed, 05 Oct 2016 19:24:47 GMT

New page: '''Unreleased structure''' The entry 5lzl is ON HOLD Authors: Azim, N., Erskine, P.T., Guo, J., Cooper, J.B. Description: Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase [[...

New page

'''Unreleased structure'''

The entry 5lzl is ON HOLD

Authors: Azim, N., Erskine, P.T., Guo, J., Cooper, J.B.

Description: Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase
[[Category: Unreleased Structures]]
[[Category: Guo, J]]
[[Category: Erskine, P.T]]
[[Category: Azim, N]]
[[Category: Cooper, J.B]]