4zm3 - Revision history

OCA at 15:45, 8 November 2023

2023-11-08T15:45:58Z

←Older revision		Revision as of 15:45, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4zm3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_pactum Streptomyces pactum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZM3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4zm3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_pactum Streptomyces pactum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZM3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.27Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=4zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zm3 OCA], [https://pdbe.org/4zm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zm3 RCSB], [https://www.ebi.ac.uk/pdbsum/4zm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zm3 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=4zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zm3 OCA], [https://pdbe.org/4zm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zm3 RCSB], [https://www.ebi.ac.uk/pdbsum/4zm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zm3 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:32, 18 May 2023

2023-05-18T07:32:57Z

←Older revision		Revision as of 07:32, 18 May 2023
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	<StructureSection load='4zm3' size='340' side='right'caption='[[4zm3]], [[Resolution\|resolution]] 2.27Å' scene=''>		<StructureSection load='4zm3' size='340' side='right'caption='[[4zm3]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zm3]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"streptomyces_pactum_var._pactum"_bhuyan_et_al._1962 "streptomyces~~ pactum ~~var. pactum" bhuyan et al. 1962~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZM3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ZM3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zm3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_pactum Streptomyces pactum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZM3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zm4\|4zm4]]</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=4zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zm3 OCA], [https://pdbe.org/4zm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zm3 RCSB], [https://www.ebi.ac.uk/pdbsum/4zm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zm3 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pctV, ptmT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=68249 "Streptomyces pactum var. pactum" Bhuyan et al. 1962])</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=4zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zm3 OCA], [~~http~~://pdbe.org/4zm3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4zm3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4zm3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4zm3 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A8R0K5_9ACTN A8R0K5_9ACTN]
	<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: Streptomyces pactum var. pactum bhuyan et al. 1962]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Eguchi, T]]	+	[[Category: Streptomyces pactum]]
-	[[Category: Hirayama, A]]	+	[[Category: Eguchi T]]
-	[[Category: Kudo, F]]	+	[[Category: Hirayama A]]
-	[[Category: Miyanaga, A]]	+	[[Category: Kudo F]]
-	~~[[Category: Aminotransferase]]~~	+	[[Category: Miyanaga A]]
-	~~[[Category: Pyridoxal 5-phosphate]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:35, 26 June 2019

2019-06-26T08:35:14Z

←Older revision		Revision as of 08:35, 26 June 2019
Line 1:		Line 1:
		+
	==Crystal structure of PLP-Dependent 3-Aminobenzoate Synthase PctV wild-type==		==Crystal structure of PLP-Dependent 3-Aminobenzoate Synthase PctV wild-type==
-	<StructureSection load='4zm3' size='340' side='right' caption='[[4zm3]], [[Resolution\|resolution]] 2.27Å' scene=''>	+	<StructureSection load='4zm3' size='340' side='right'caption='[[4zm3]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zm3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZM3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zm3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_pactum_var._pactum"_bhuyan_et_al._1962 "streptomyces pactum var. pactum" bhuyan et al. 1962]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZM3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zm4\|4zm4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zm4\|4zm4]]</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=4zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zm3 OCA], [http://pdbe.org/4zm3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zm3 RCSB], [http://www.ebi.ac.uk/pdbsum/4zm3 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pctV, ptmT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=68249 "Streptomyces pactum var. pactum" Bhuyan et al. 1962])</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=4zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zm3 OCA], [http://pdbe.org/4zm3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zm3 RCSB], [http://www.ebi.ac.uk/pdbsum/4zm3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zm3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Streptomyces pactum var. pactum bhuyan et al. 1962]]
		+	[[Category: Large Structures]]
	[[Category: Eguchi, T]]		[[Category: Eguchi, T]]
	[[Category: Hirayama, A]]		[[Category: Hirayama, A]]

OCA at 03:57, 16 October 2015

2015-10-16T03:57:27Z

←Older revision		Revision as of 03:57, 16 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of PLP-Dependent 3-Aminobenzoate Synthase PctV wild-type==
		+	<StructureSection load='4zm3' size='340' side='right' caption='[[4zm3]], [[Resolution\|resolution]] 2.27Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4zm3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZM3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zm4\|4zm4]]</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=4zm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zm3 OCA], [http://pdbe.org/4zm3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zm3 RCSB], [http://www.ebi.ac.uk/pdbsum/4zm3 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mutational analysis of the pyridoxal 5'-phosphate (PLP)-dependent enzyme PctV has been carried out to elucidate the multi-step reaction mechanism for the formation of 3-aminobenzoate (3-ABA) from 3-dehydroshikimate (3-DSA). The results revealed that the introduction of a K276R mutation led to the accumulation of a quinonoid intermediate with an absorption maximum of 580 nm following the reaction of pyridoxamine 5'-phosphate (PMP) with 3-DSA. Furthermore, the chemical structure of this intermediate was supported by X-ray crystallographic analysis of the complex formed between the K276R mutant and the quinonoid intermediate. These results clearly show that a quinonoid intermediate is involved in the formation of 3-ABA, and also indicate that the Lys276 residue in the active site of the PctV enzyme plays multiple roles including acid/base catalysis during the dehydration reaction of the quinonoid intermediate, as well as assisting in the PMP formation and aminotransfer reaction.

-	~~The entry 4zm3 is ON HOLD until Paper Publication~~	+	Mechanism-based Trapping of the Quinonoid Intermediate Using the K276R Mutant of PLP-Dependent 3-Aminobenzoate Synthase PctV in the Biosynthesis of Pactamycin.,Hirayama A, Miyanaga A, Kudo F, Eguchi T Chembiochem. 2015 Oct 1. doi: 10.1002/cbic.201500426. PMID:26426567<ref>PMID:26426567</ref>

-	~~Authors: Hirayama~~, A.~~, Miyanaga, A~~.~~, Kudo, F., Eguchi, T~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of PLP~~-~~Dependent 3~~-~~Aminobenzoate Synthase PctV wild-type~~	+	<div class="pdbe-citations 4zm3" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Eguchi, T]]
		+	[[Category: Hirayama, A]]
	[[Category: Kudo, F]]		[[Category: Kudo, F]]
-	[[Category: Hirayama, A]]
-	[[Category: Eguchi, T]]
	[[Category: Miyanaga, A]]		[[Category: Miyanaga, A]]
		+	[[Category: Aminotransferase]]
		+	[[Category: Pyridoxal 5-phosphate]]
		+	[[Category: Transferase]]

OCA at 11:00, 3 June 2015

2015-06-03T11:00:08Z

←Older revision		Revision as of 11:00, 3 June 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4zm3 is ON HOLD	+	The entry 4zm3 is ON HOLD until Paper Publication

	Authors: Hirayama, A., Miyanaga, A., Kudo, F., Eguchi, T.		Authors: Hirayama, A., Miyanaga, A., Kudo, F., Eguchi, T.

OCA: Protected "4zm3" [edit=sysop:move=sysop]

2015-05-13T11:07:02Z

Protected "4zm3" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:07, 13 May 2015

OCA: New page: '''Unreleased structure''' The entry 4zm3 is ON HOLD Authors: Hirayama, A., Miyanaga, A., Kudo, F., Eguchi, T. Description: Crystal structure of PLP-Dependent 3-Aminobenzoate Synthase ...

2015-05-13T11:07:01Z

New page: '''Unreleased structure''' The entry 4zm3 is ON HOLD Authors: Hirayama, A., Miyanaga, A., Kudo, F., Eguchi, T. Description: Crystal structure of PLP-Dependent 3-Aminobenzoate Synthase ...

New page

'''Unreleased structure'''

The entry 4zm3 is ON HOLD

Authors: Hirayama, A., Miyanaga, A., Kudo, F., Eguchi, T.

Description: Crystal structure of PLP-Dependent 3-Aminobenzoate Synthase PctV wild-type
[[Category: Unreleased Structures]]
[[Category: Kudo, F]]
[[Category: Hirayama, A]]
[[Category: Eguchi, T]]
[[Category: Miyanaga, A]]