5cj3 - Revision history

OCA at 08:38, 27 September 2023

OCA — Wed, 27 Sep 2023 08:38:19 GMT

←Older revision		Revision as of 08:38, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_pilosus Streptomyces pilosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CJ3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_pilosus Streptomyces pilosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CJ3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=52G:ZORBAMYCIN'>52G</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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]] 1.6499Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=52G:ZORBAMYCIN'>52G</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=5cj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cj3 OCA], [https://pdbe.org/5cj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cj3 RCSB], [https://www.ebi.ac.uk/pdbsum/5cj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cj3 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=5cj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cj3 OCA], [https://pdbe.org/5cj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cj3 RCSB], [https://www.ebi.ac.uk/pdbsum/5cj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cj3 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:08, 14 June 2023

OCA — Wed, 14 Jun 2023 12:08:35 GMT

←Older revision		Revision as of 12:08, 14 June 2023
Line 1:		Line 1:

	==Crystal structure of the zorbamycin binding protein (ZbmA) from Streptomyces flavoviridis with zorbamycin==		==Crystal structure of the zorbamycin binding protein (ZbmA) from Streptomyces flavoviridis with zorbamycin==
-	<StructureSection load='5cj3' size='340' side='right' caption='[[5cj3]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='5cj3' size='340' side='right'caption='[[5cj3]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5cj3]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"actinomyces_flavoviridis"_preobrazhenskaya_et_al._in_gauze_et_al._1957 "actinomyces flavoviridis" preobrazhenskaya et al. in gauze et al. 1957~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CJ3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CJ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5cj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_pilosus Streptomyces pilosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CJ3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=52G:ZORBAMYCIN'>52G</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=52G:ZORBAMYCIN'>52G</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iag\|4iag]]</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=5cj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cj3 OCA], [https://pdbe.org/5cj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cj3 RCSB], [https://www.ebi.ac.uk/pdbsum/5cj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cj3 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">zbmA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=66889 "Actinomyces flavoviridis" Preobrazhenskaya et al. in Gauze et al. 1957])</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=5cj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cj3 OCA], [~~http~~://pdbe.org/5cj3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5cj3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5cj3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5cj3 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B9UIZ4_9ACTN B9UIZ4_9ACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Actinomyces flavoviridis preobrazhenskaya et al. in gauze et al. 1957~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Babnigg, G~~]]	+	[[Category: Streptomyces pilosus]]
-	[[Category: ~~Bigelow, L~~]]	+	[[Category: Babnigg G]]
-	[[Category: ~~Biosynthesis, Enzyme Discovery for Natural Product~~]]	+	[[Category: Bigelow L]]
-	[[Category: Chang, C]]	+	[[Category: Chang C]]
-	[[Category: Chang, C Y]]	+	[[Category: Chang C-Y]]
-	[[Category: Clancy, S]]	+	[[Category: Clancy S]]
-	[[Category: ~~Joachimiak, A~~]]	+	[[Category: Enzyme Discovery for Natural Product Biosynthesis]]
-	[[Category: ~~Lohman, J R~~]]	+	[[Category: Joachimiak A]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: Lohman JR]]
-	[[Category: Ma, M]]	+	[[Category: Ma M]]
-	~~[[Category: NatPro, Enzyme Discovery for Natural Product Biosynthesis~~]]	+	[[Category: Rudolf JD]]
-	[[Category: Rudolf~~, J D~~]]	+	[[Category: Shen B]]
-	[[Category: Shen, B]]	+	[[Category: Yang D]]
-	[[Category: Yang, D]]	+
-	~~[[Category: Antibiotic binding protein-antibiotic complex]]~~	+
-	~~[[Category: Enzyme discovery for natural product biosynthesis]]~~	+
-	~~[[Category: Mcsg]]~~	+
-	~~[[Category: Natpro]]~~	+
-	~~[[Category: Psi-biology]]~~	+
-	~~[[Category: Zorbamycin]]~~	+
-	~~[[Category: Zorbamycin binding protein~~]]	+

OCA at 14:45, 16 November 2017

OCA — Thu, 16 Nov 2017 14:45:05 GMT

←Older revision		Revision as of 14:45, 16 November 2017
Line 1:		Line 1:
		+
	==Crystal structure of the zorbamycin binding protein (ZbmA) from Streptomyces flavoviridis with zorbamycin==		==Crystal structure of the zorbamycin binding protein (ZbmA) from Streptomyces flavoviridis with zorbamycin==
	<StructureSection load='5cj3' size='340' side='right' caption='[[5cj3]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='5cj3' size='340' side='right' caption='[[5cj3]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5cj3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CJ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5cj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_flavoviridis"_preobrazhenskaya_et_al._in_gauze_et_al._1957 "actinomyces flavoviridis" preobrazhenskaya et al. in gauze et al. 1957]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CJ3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=52G:ZORBAMYCIN'>52G</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=52G:ZORBAMYCIN'>52G</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iag\|4iag]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iag\|4iag]]</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=5cj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cj3 OCA], [http://pdbe.org/5cj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cj3 RCSB], [http://www.ebi.ac.uk/pdbsum/5cj3 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">zbmA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=66889 "Actinomyces flavoviridis" Preobrazhenskaya et al. in Gauze et al. 1957])</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=5cj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cj3 OCA], [http://pdbe.org/5cj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cj3 RCSB], [http://www.ebi.ac.uk/pdbsum/5cj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cj3 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: Actinomyces flavoviridis preobrazhenskaya et al. in gauze et al. 1957]]
	[[Category: Babnigg, G]]		[[Category: Babnigg, G]]
	[[Category: Bigelow, L]]		[[Category: Bigelow, L]]

OCA at 20:41, 30 November 2015

OCA — Mon, 30 Nov 2015 20:41:14 GMT

←Older revision		Revision as of 20:41, 30 November 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=52G:ZORBAMYCIN'>52G</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=52G:ZORBAMYCIN'>52G</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iag\|4iag]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iag\|4iag]]</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=5cj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5cj3 RCSB], [http://www.ebi.ac.uk/pdbsum/5cj3 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=5cj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cj3 OCA], [http://pdbe.org/5cj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cj3 RCSB], [http://www.ebi.ac.uk/pdbsum/5cj3 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The bleomycins (BLMs), tallysomycins (TLMs), phleomycin, and zorbamycin (ZBM) are members of the BLM family of glycopeptide-derived antitumor antibiotics. The BLM-producing Streptomyces verticillus ATCC15003 and the TLM-producing Streptoalloteichus hindustanus E465-94 ATCC31158 both possess at least two self-resistance elements, an N-acetyltransferase and a binding protein. The N-acetyltransferase provides resistance by disrupting the metal-binding domain of the antibiotic that is required for activity, while the binding protein confers resistance by sequestering the metal-bound antibiotic and preventing drug activation via molecular oxygen. We recently established that the ZBM producer, Streptomyces flavoviridis ATCC21892, lacks the N-acetyltransferase resistance gene and that the ZBM-binding protein, ZbmA, is sufficient to confer resistance in the producing strain. To investigate the resistance mechanism attributed to ZbmA, we determined the crystal structures of apo and Cu(II)-ZBM-bound ZbmA at high resolutions of 1.90 and 1.65 A, respectively. A comparison and contrast with other structurally characterized members of the BLM-binding protein family revealed key differences in the protein-ligand binding environment that fine-tunes the ability of ZbmA to sequester metal-bound ZBM and supports drug sequestration as the primary resistance mechanism in the producing organisms of the BLM family of antitumor antibiotics.
		+
		+	Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892.,Rudolf JD, Bigelow L, Chang C, Cuff ME, Lohman JR, Chang CY, Ma M, Yang D, Clancy S, Babnigg G, Joachimiak A, Phillips GN Jr, Shen B Biochemistry. 2015 Nov 17;54(45):6842-51. doi: 10.1021/acs.biochem.5b01008. Epub , 2015 Nov 5. PMID:26512730<ref>PMID:26512730</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5cj3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA: Protected "5cj3" [edit=sysop:move=sysop]

OCA — Wed, 22 Jul 2015 14:21:29 GMT

Protected "5cj3" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:21, 22 July 2015

OCA: New page: ==Crystal structure of the zorbamycin binding protein (ZbmA) from Streptomyces flavoviridis with zorbamycin== == Structural highlights ==
<table><tr><td colspan='2'>[[5cj3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CJ3 OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CJ3 FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=52G:ZORBAMYCIN'>52G</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[4iag|4iag]]</td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5cj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5cj3 RCSB], [http://www.ebi.ac.uk/pdbsum/5cj3 PDBsum]</td></tr>
</table>
TOC
</StructureSection>
[[Category: Babnigg, G]]
[[Category: Bigelow, L]]
[[Category: Biosynthesis, Enzyme Discovery for Natural Product]]
[[Category: Chang, C]]
[[Category: Chang, C Y]]
[[Category: Clancy, S]]
[[Category: Joachimiak, A]]
[[Category: Lohman, J R]]
[[Category: Structural genomic]]
[[Category: Ma, M]]
[[Category: NatPro, Enzyme Discovery for Natural Product Biosynthesis]]
[[Category: Rudolf, J D]]
[[Category: Shen, B]]
[[Category: Yang, D]]
[[Category: Antibiotic binding protein-antibiotic complex]]
[[Category: Enzyme discovery for natural product biosynthesis]]
[[Category: Mcsg]]
[[Category: Natpro]]
[[Category: Psi-biology]]
[[Category: Zorbamycin]]
[[Category: Zorbamycin binding protein]]