5h6t - Revision history

OCA at 07:25, 9 August 2023

OCA — Wed, 09 Aug 2023 07:25:35 GMT

←Older revision		Revision as of 07:25, 9 August 2023
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	<StructureSection load='5h6t' size='340' side='right'caption='[[5h6t]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5h6t' size='340' side='right'caption='[[5h6t]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h6t]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Microbacterium_sp.~~_hm58~~-2 Microbacterium sp. ~~hm58~~-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H6T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5H6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h6t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Microbacterium_sp._HM58-2 Microbacterium sp. HM58-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H6T FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5h6s\|5h6s]]</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]] 1.6Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">MHM582_3487 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1778770 Microbacterium sp. HM58-2])~~</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=5h6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h6t OCA], [https://pdbe.org/5h6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h6t RCSB], [https://www.ebi.ac.uk/pdbsum/5h6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h6t 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=5h6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h6t OCA], [~~http~~://pdbe.org/5h6t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5h6t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5h6t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5h6t ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Microbacterium sp. ~~hm58~~-2]]	+	[[Category: Microbacterium sp. HM58-2]]
-	[[Category: Akiyama, T]]	+	[[Category: Akiyama T]]
-	[[Category: Ishii, M]]	+	[[Category: Ishii M]]
-	[[Category: Oinuma, K]]	+	[[Category: Oinuma K]]
-	[[Category: Sasaki, Y]]	+	[[Category: Sasaki Y]]
-	[[Category: Takaya, N]]	+	[[Category: Takaya N]]
-	[[Category: Takuwa, A]]	+	[[Category: Takuwa A]]
-	[[Category: Yajima, S]]	+	[[Category: Yajima S]]
-	~~[[Category: Amidase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:12, 26 February 2020

OCA — Wed, 26 Feb 2020 10:12:52 GMT

←Older revision		Revision as of 10:12, 26 February 2020
Line 1:		Line 1:

	==Crystal structure of Hydrazidase from Microbacterium sp. strain HM58-2==		==Crystal structure of Hydrazidase from Microbacterium sp. strain HM58-2==
-	<StructureSection load='5h6t' size='340' side='right' caption='[[5h6t]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5h6t' size='340' side='right'caption='[[5h6t]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h6t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h6t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Microbacterium_sp._hm58-2 Microbacterium sp. hm58-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H6T FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h6s\|5h6s]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h6s\|5h6s]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MHM582_3487 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1778770 Microbacterium sp. HM58-2])</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=5h6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h6t OCA], [http://pdbe.org/5h6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h6t RCSB], [http://www.ebi.ac.uk/pdbsum/5h6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h6t 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=5h6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h6t OCA], [http://pdbe.org/5h6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h6t RCSB], [http://www.ebi.ac.uk/pdbsum/5h6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h6t ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Microbacterium sp. hm58-2]]
	[[Category: Akiyama, T]]		[[Category: Akiyama, T]]
	[[Category: Ishii, M]]		[[Category: Ishii, M]]

OCA at 21:10, 15 March 2017

OCA — Wed, 15 Mar 2017 21:10:57 GMT

←Older revision		Revision as of 21:10, 15 March 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5h6t is ~~ON HOLD~~	+	==Crystal structure of Hydrazidase from Microbacterium sp. strain HM58-2==
		+	<StructureSection load='5h6t' size='340' side='right' caption='[[5h6t]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5h6t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H6T FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h6s\|5h6s]]</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=5h6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h6t OCA], [http://pdbe.org/5h6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h6t RCSB], [http://www.ebi.ac.uk/pdbsum/5h6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h6t ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hydrazidase was an enzyme that remained unidentified for a half century. However, recently, it was purified, and its encoding gene was cloned. Microbacterium sp. strain HM58-2 grows with acylhydrazides as its sole carbon source; it produces hydrazidase and degrades acylhydrazides to acetate and hydrazides. The bacterial hydrazidase belongs to the amidase signature enzyme family and contains a Ser-cisSer-Lys catalytic motif. The condensation of hydrazine and carbonic acid produces various hydrazides, some of which are raw materials for synthesizing pharmaceuticals and other useful chemicals. Although natural hydrazide compounds have been identified, the metabolic systems for hydrazides are not fully understood. Here, we report the crystal structure of hydrazidase from Microbacterium sp. strain HM58-2. The active site was revealed to consist of a Ser-cisSer-Lys catalytic triad, in which Ser179 forms a covalent bond with a carbonyl carbon of the substrate. 4-Hydroxybenzoic acid hydrazide bound to the S179A mutant, showing an oxyanion hole composed of the three backbone amide groups. Furthermore, H336 in the non-conserved region in the amidase family may define the substrate specificity, which was confirmed by mutation analysis. A wild-type apoenzyme structure revealed an unidentified molecule covalently bound to S179, representing a tetrahedral intermediate.

-	~~Authors: Akiyama~~, T., ~~Ishii~~, M., Takuwa, A., Oinuma~~, K.~~, Sasaki, Y., Takaya, N., Yajima, S.	+	Structural basis of the substrate recognition of hydrazidase isolated from Microbacterium sp. strain HM58-2, which catalyzes acylhydrazide compounds as its sole carbon source.,Akiyama T, Ishii M, Takuwa A, Oinuma KI, Sasaki Y, Takaya N, Yajima S Biochem Biophys Res Commun. 2017 Jan 22;482(4):1007-1012. doi:, 10.1016/j.bbrc.2016.11.148. Epub 2016 Nov 28. PMID:27908731<ref>PMID:27908731</ref>

-	~~Description: Crystal structure~~ of ~~Hydrazidase from Microbacterium sp~~. ~~strain HM58-2~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Takuwa~~, A]]	+	<div class="pdbe-citations 5h6t" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Akiyama, T]]
	[[Category: Ishii, M]]		[[Category: Ishii, M]]
-	[[Category: Yajima, S]]
-	[[Category: Takaya, N]]
-	[[Category: Sasaki, Y]]
	[[Category: Oinuma, K]]		[[Category: Oinuma, K]]
-	[[Category: ~~Akiyama~~, T]]	+	[[Category: Sasaki, Y]]
		+	[[Category: Takaya, N]]
		+	[[Category: Takuwa, A]]
		+	[[Category: Yajima, S]]
		+	[[Category: Amidase]]
		+	[[Category: Hydrolase]]

OCA at 09:27, 9 March 2017

OCA — Thu, 09 Mar 2017 09:27:23 GMT

←Older revision		Revision as of 09:27, 9 March 2017
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	Description: Crystal structure of Hydrazidase from Microbacterium sp. strain HM58-2		Description: Crystal structure of Hydrazidase from Microbacterium sp. strain HM58-2
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Takuwa, A]]
	[[Category: Ishii, M]]		[[Category: Ishii, M]]
	[[Category: Yajima, S]]		[[Category: Yajima, S]]
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	[[Category: Sasaki, Y]]		[[Category: Sasaki, Y]]
	[[Category: Oinuma, K]]		[[Category: Oinuma, K]]
-	[[Category: Takuwa, A]]
	[[Category: Akiyama, T]]		[[Category: Akiyama, T]]

OCA: Protected "5h6t" [edit=sysop:move=sysop]

OCA — Fri, 09 Dec 2016 13:48:58 GMT

Protected "5h6t" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:48, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5h6t is ON HOLD Authors: Akiyama, T., Ishii, M., Takuwa, A., Oinuma, K., Sasaki, Y., Takaya, N., Yajima, S. Description: Crystal structure of Hydra...

OCA — Fri, 09 Dec 2016 13:48:57 GMT

New page: '''Unreleased structure''' The entry 5h6t is ON HOLD Authors: Akiyama, T., Ishii, M., Takuwa, A., Oinuma, K., Sasaki, Y., Takaya, N., Yajima, S. Description: Crystal structure of Hydra...

New page

'''Unreleased structure'''

The entry 5h6t is ON HOLD

Authors: Akiyama, T., Ishii, M., Takuwa, A., Oinuma, K., Sasaki, Y., Takaya, N., Yajima, S.

Description: Crystal structure of Hydrazidase from Microbacterium sp. strain HM58-2
[[Category: Unreleased Structures]]
[[Category: Ishii, M]]
[[Category: Yajima, S]]
[[Category: Takaya, N]]
[[Category: Sasaki, Y]]
[[Category: Oinuma, K]]
[[Category: Takuwa, A]]
[[Category: Akiyama, T]]