3vsd - Revision history

OCA at 22:50, 26 March 2025

2025-03-26T22:50:16Z

← Older revision		Revision as of 22:50, 26 March 2025
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	<StructureSection load='3vsd' size='340' side='right'caption='[[3vsd]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='3vsd' size='340' side='right'caption='[[3vsd]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vsd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aerpe Aerpe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VSD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vsd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VSD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OAS:O-ACETYLSERINE'>OAS</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]] 2.09Å</td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wkv\|1wkv]], [[3vsa\|3vsa]], [[3vsc\|3vsc]]</div></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OAS:O-ACETYLSERINE'>OAS</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APE1586, APE_1586, cysO ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</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=3vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsd OCA], [https://pdbe.org/3vsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vsd RCSB], [https://www.ebi.ac.uk/pdbsum/3vsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vsd 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=3vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsd OCA], [https://pdbe.org/3vsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vsd RCSB], [https://www.ebi.ac.uk/pdbsum/3vsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vsd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/CYSO_AERPE CYSO_AERPE]] Cysteine synthase that can also catalyze the synthesis of S-sulfo-L-cysteine from thiosulfate and O(3)-acetyl-L-serine, as well as the sulfhydrylation of L-serine by sulfide.<ref>PMID:12644499</ref>		[https://www.uniprot.org/uniprot/CYSO_AERPE CYSO_AERPE] Cysteine synthase that can also catalyze the synthesis of S-sulfo-L-cysteine from thiosulfate and O(3)-acetyl-L-serine, as well as the sulfhydrylation of L-serine by sulfide.<ref>PMID:12644499</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: ~~Aerpe~~]]		[[Category: Aeropyrum pernix K1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ishikawa, K]]		[[Category: Ishikawa K]]
	[[Category: Kataoka, M]]		[[Category: Kataoka M]]
	[[Category: Kawai, Y]]		[[Category: Kawai Y]]
	[[Category: Nakamura, T]]		[[Category: Nakamura T]]
	~~[[Category: Cysteine biosynthesis]]~~
	~~[[Category: External schiff base of plp with o-acetylserine]]~~
	~~[[Category: K127a mutant]]~~
	~~[[Category: Transferase~~]]

OCA at 19:01, 27 July 2022

2022-07-27T19:01:26Z

← Older revision		Revision as of 19:01, 27 July 2022
Line 1:		Line 1:

	==Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine==		==Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine==
	<StructureSection load='3vsd' size='340' side='right' caption='[[3vsd]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='3vsd' size='340' side='right'caption='[[3vsd]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vsd]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VSD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vsd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VSD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OAS:O-ACETYLSERINE'>OAS</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OAS:O-ACETYLSERINE'>OAS</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">[[1wkv\|1wkv]], [[3vsa\|3vsa]], [[3vsc\|3vsc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wkv\|1wkv]], [[3vsa\|3vsa]], [[3vsc\|3vsc]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APE1586, APE_1586, cysO ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APE1586, APE_1586, cysO ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</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=3vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsd OCA], [~~http~~://pdbe.org/3vsd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vsd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vsd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vsd 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=3vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsd OCA], [https://pdbe.org/3vsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vsd RCSB], [https://www.ebi.ac.uk/pdbsum/3vsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vsd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/CYSO_AERPE CYSO_AERPE]] Cysteine synthase that can also catalyze the synthesis of S-sulfo-L-cysteine from thiosulfate and O(3)-acetyl-L-serine, as well as the sulfhydrylation of L-serine by sulfide.<ref>PMID:12644499</ref>		[[https://www.uniprot.org/uniprot/CYSO_AERPE CYSO_AERPE]] Cysteine synthase that can also catalyze the synthesis of S-sulfo-L-cysteine from thiosulfate and O(3)-acetyl-L-serine, as well as the sulfhydrylation of L-serine by sulfide.<ref>PMID:12644499</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Aerpe]]		[[Category: Aerpe]]
			[[Category: Large Structures]]
	[[Category: Ishikawa, K]]		[[Category: Ishikawa, K]]
	[[Category: Kataoka, M]]		[[Category: Kataoka, M]]

OCA at 07:57, 22 November 2017

2017-11-22T07:57:30Z

← Older revision		Revision as of 07:57, 22 November 2017
Line 7:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkv\|1wkv]], [[3vsa\|3vsa]], [[3vsc\|3vsc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkv\|1wkv]], [[3vsa\|3vsa]], [[3vsc\|3vsc]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APE1586, APE_1586, cysO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APE1586, APE_1586, cysO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</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=3vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsd OCA], [http://pdbe.org/3vsd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vsd RCSB], [http://www.ebi.ac.uk/pdbsum/3vsd 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=3vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsd OCA], [http://pdbe.org/3vsd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vsd RCSB], [http://www.ebi.ac.uk/pdbsum/3vsd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vsd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 16:06, 10 May 2016

2016-05-10T16:06:13Z

← Older revision		Revision as of 16:06, 10 May 2016
Line 1:		Line 1:

	==Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine==		==Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine==
	<StructureSection load='3vsd' size='340' side='right' caption='[[3vsd]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='3vsd' size='340' side='right' caption='[[3vsd]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vsd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aeropyrum_pernix Aeropyrum pernix~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VSD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vsd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VSD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OAS:O-ACETYLSERINE'>OAS</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OAS:O-ACETYLSERINE'>OAS</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">[[1wkv\|1wkv]], [[3vsa\|3vsa]], [[3vsc\|3vsc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkv\|1wkv]], [[3vsa\|3vsa]], [[3vsc\|3vsc]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APE1586, APE_1586, cysO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~56636 Aeropyrum pernix~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APE1586, APE_1586, cysO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</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=3vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vsd RCSB], [http://www.ebi.ac.uk/pdbsum/3vsd 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=3vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsd OCA], [http://pdbe.org/3vsd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vsd RCSB], [http://www.ebi.ac.uk/pdbsum/3vsd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	O-~~Phosphoserine~~ sulfhydrylase is a ~~new~~ enzyme ~~found in a~~ hyperthermophilic archaeon, Aeropyrum pernix K1. ~~This enzyme catalyzes a novel cysteine synthetic reaction from~~ O-phospho-l-serine ~~and sulfide~~. ~~The crystal structure~~ of the enzyme ~~was determined at 2~~.~~0A resolution using the method of multi~~-~~wavelength anomalous dispersion. A monomer consists~~ of ~~three domains, including~~ an N-~~terminal domain with a new alpha/beta fold~~. ~~The topology folds~~ of the ~~middle and C-terminal domains were similar to those of~~ the ~~O-acetylserine sulfhydrylase-A from Salmonella typhimurium and~~ the ~~cystathionine beta-synthase from human. The cofactor,~~ pyridoxal 5'-phosphate, ~~is bound~~ in ~~a cleft~~ between the ~~middle~~ and ~~C-terminal domains through~~ a ~~covalent linkage~~ to ~~Lys127~~. ~~Based on the structure determined~~, ~~O-phospho-l-serine could be rationally modeled into~~ the ~~active site~~ of the ~~enzyme. An enzyme-substrate~~ complex ~~model and a mutation experiment revealed that Arg297, unique to hyperthermophilic archaea, is one~~ of the ~~most crucial residues~~ for ~~O-phosphoserine sulfhydrylation activity~~. ~~There are more hydrophobic areas and less electric charges at~~ the ~~dimer interface, compared to~~ the ~~S.typhimurium O-acetylserine sulfhydrylase~~.		L-Cysteine is synthesized from O-acetyl-L-serine (OAS) and sulfide by O-acetylserine sulfhydrylase (OASS; EC 2.5.1.47) in plants and bacteria. O-phosphoserine sulfhydrylase (OPSS; EC 2.5.1.65) is a novel enzyme from the hyperthermophilic aerobic archaeon Aeropyrum pernix K1 (2003). OPSS can use OAS or O-phospho-L-serine (OPS) to synthesize L-cysteine. To elucidate the mechanism of the substrate specificity of OPSS, we analyzed three-dimensional structures of the active site of the enzyme. The active-site lysine (K127) of OPSS forms an internal Schiff base with pyridoxal 5'-phosphate. Therefore, crystals of the complexes formed by the K127A mutant with the external Schiff base of pyridoxal 5'-phosphate with either OPS or OAS were prepared and examined by X-ray diffraction analysis. In contrast to that observed for OASS, no significant difference was seen in the overall structure between the free and complexed forms of OPSS. The side chains of T152, S153, and Q224 interacted with the carboxylate of the substrates, as a previous study has suggested. The side chain of R297 has been proposed to recognize the phosphate group of OPS. Surprisingly, however, the position of R297 was significantly unchanged in the complex of the OPSS K127A mutant with the external Schiff base, allowing enough space for an interaction with OPS. The positively charged environment around the entrance of the active site including S153 and R297 is important for accepting negatively charged substrates such as OPS.

	~~Three-dimensional structure~~ of ~~a new enzyme,~~ O-phosphoserine sulfhydrylase~~, involved in l-cysteine biosynthesis by a~~ hyperthermophilic archaeon, Aeropyrum pernix K1, ~~at 2.0A resolution.~~,~~Oda~~ Y, ~~Mino~~ K, ~~Ishikawa~~ K, ~~Ataka~~ M J Mol Biol. ~~2005 Aug 12~~;~~351~~(2):~~334~~-44. PMID:~~16005886~~<ref>PMID:~~16005886~~</ref>		Structural analysis of the substrate recognition mechanism in O-phosphoserine sulfhydrylase from the hyperthermophilic archaeon Aeropyrum pernix K1.,Nakamura T, Kawai Y, Kunimoto K, Iwasaki Y, Nishii K, Kataoka M, Ishikawa K J Mol Biol. 2012 Sep 7;422(1):33-44. Epub 2012 May 11. PMID:22580223<ref>PMID:22580223</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 3vsd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Aeropyrum pernix~~]]		[[Category: Aerpe]]
	[[Category: Ishikawa, K]]		[[Category: Ishikawa, K]]
	[[Category: Kataoka, M]]		[[Category: Kataoka, M]]

OCA at 06:48, 24 December 2014

2014-12-24T06:48:21Z

← Older revision		Revision as of 06:48, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vsd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VSD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vsd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VSD FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OAS:O-ACETYLSERINE'>OAS</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OAS:O-ACETYLSERINE'>OAS</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkv\|1wkv]], [[3vsa\|3vsa]], [[3vsc\|3vsc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkv\|1wkv]], [[3vsa\|3vsa]], [[3vsc\|3vsc]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APE1586, APE_1586, cysO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 Aeropyrum pernix])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APE1586, APE_1586, cysO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 Aeropyrum pernix])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vsd RCSB], [http://www.ebi.ac.uk/pdbsum/3vsd 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=3vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vsd RCSB], [http://www.ebi.ac.uk/pdbsum/3vsd PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/CYSO_AERPE CYSO_AERPE]] Cysteine synthase that can also catalyze the synthesis of S-sulfo-L-cysteine from thiosulfate and O(3)-acetyl-L-serine, as well as the sulfhydrylation of L-serine by sulfide.<ref>PMID:12644499</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 16:
	Three-dimensional structure of a new enzyme, O-phosphoserine sulfhydrylase, involved in l-cysteine biosynthesis by a hyperthermophilic archaeon, Aeropyrum pernix K1, at 2.0A resolution.,Oda Y, Mino K, Ishikawa K, Ataka M J Mol Biol. 2005 Aug 12;351(2):334-44. PMID:16005886<ref>PMID:16005886</ref>		Three-dimensional structure of a new enzyme, O-phosphoserine sulfhydrylase, involved in l-cysteine biosynthesis by a hyperthermophilic archaeon, Aeropyrum pernix K1, at 2.0A resolution.,Oda Y, Mino K, Ishikawa K, Ataka M J Mol Biol. 2005 Aug 12;351(2):334-44. PMID:16005886<ref>PMID:16005886</ref>

	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Ishikawa, K.]]		[[Category: Ishikawa, K]]
	[[Category: Kataoka, M.]]		[[Category: Kataoka, M]]
	[[Category: Kawai, Y.]]		[[Category: Kawai, Y]]
	[[Category: Nakamura, T.]]		[[Category: Nakamura, T]]
	[[Category: Cysteine biosynthesis]]		[[Category: Cysteine biosynthesis]]
	[[Category: External schiff base of plp with o-acetylserine]]		[[Category: External schiff base of plp with o-acetylserine]]
	[[Category: K127a mutant]]		[[Category: K127a mutant]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 07:19, 5 June 2014

2014-06-05T07:19:05Z

← Older revision		Revision as of 07:19, 5 June 2014
Line 1:		Line 1:
	[[~~Image~~:~~3vsd~~.~~jpg~~\|~~left~~\|~~200px~~]]		==Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine==
			<StructureSection load='3vsd' size='340' side='right' caption='[[3vsd]], [[Resolution\|resolution]] 2.09Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3vsd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VSD FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OAS:O-ACETYLSERINE'>OAS</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkv\|1wkv]], [[3vsa\|3vsa]], [[3vsc\|3vsc]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APE1586, APE_1586, cysO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 Aeropyrum pernix])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vsd RCSB], [http://www.ebi.ac.uk/pdbsum/3vsd PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			O-Phosphoserine sulfhydrylase is a new enzyme found in a hyperthermophilic archaeon, Aeropyrum pernix K1. This enzyme catalyzes a novel cysteine synthetic reaction from O-phospho-l-serine and sulfide. The crystal structure of the enzyme was determined at 2.0A resolution using the method of multi-wavelength anomalous dispersion. A monomer consists of three domains, including an N-terminal domain with a new alpha/beta fold. The topology folds of the middle and C-terminal domains were similar to those of the O-acetylserine sulfhydrylase-A from Salmonella typhimurium and the cystathionine beta-synthase from human. The cofactor, pyridoxal 5'-phosphate, is bound in a cleft between the middle and C-terminal domains through a covalent linkage to Lys127. Based on the structure determined, O-phospho-l-serine could be rationally modeled into the active site of the enzyme. An enzyme-substrate complex model and a mutation experiment revealed that Arg297, unique to hyperthermophilic archaea, is one of the most crucial residues for O-phosphoserine sulfhydrylation activity. There are more hydrophobic areas and less electric charges at the dimer interface, compared to the S.typhimurium O-acetylserine sulfhydrylase.

	<!--		Three-dimensional structure of a new enzyme, O-phosphoserine sulfhydrylase, involved in l-cysteine biosynthesis by a hyperthermophilic archaeon, Aeropyrum pernix K1, at 2.0A resolution.,Oda Y, Mino K, Ishikawa K, Ataka M J Mol Biol. 2005 Aug 12;351(2):334-44. PMID:16005886<ref>PMID:16005886</ref>
	~~The line below this paragraph~~, ~~containing "STRUCTURE_3vsd"~~, ~~creates the "Structure Box" on the page~~.
	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display~~.
	-->
	~~{{STRUCTURE_3vsd\| PDB=3vsd \| SCENE= }}~~

	~~===Crystal Structure~~ of the ~~K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine===~~		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
			</div>
			== References ==
	~~<!--~~		<references/>
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16005886}}, adds the Publication Abstract to the page~~		__TOC__
	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 16005886 is the PubMed ID number~~.		</StructureSection>
	-->
	~~{{ABSTRACT_PUBMED_16005886}}~~

	~~==About this Structure==~~
	~~[[3vsd]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSD OCA].~~

	==~~Reference~~==
	<~~ref group="xtra">PMID:016005886<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Ishikawa, K.]]		[[Category: Ishikawa, K.]]

OCA at 09:21, 16 May 2012

2012-05-16T09:21:05Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:3vsd.jpg|left|200px]]
-The entry 3vsd is ON HOLD
+<!--
-Authors: Nakamura, T., Kawai, Y., Kataoka, M., Ishikawa, K.
+===Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine===
-Description: Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine

OCA at 08:38, 9 May 2012

2012-05-09T08:38:41Z

← Older revision		Revision as of 08:38, 9 May 2012
Line 3:		Line 3:
	The entry 3vsd is ON HOLD		The entry 3vsd is ON HOLD

	Authors: ~~Takashi~~ Nakamura, ~~Yoshito~~ Kawai, ~~Misumi~~ Kataoka, ~~Kazuhiko~~ Ishikawa		Authors: Nakamura, T., Kawai, Y., Kataoka, M., Ishikawa, K.

	Description: Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine		Description: Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine

OCA: Protected "3vsd" [edit=sysop:move=sysop]

2012-05-02T18:47:05Z

Protected "3vsd" [edit=sysop:move=sysop]

← Older revision	Revision as of 18:47, 2 May 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 3vsd is ON HOLD Authors: Takashi Nakamura, Yoshito Kawai, Misumi Kataoka, Kazuhiko Ishikawa Description: Crystal Structure of the K127A Mutant of O...

2012-05-02T18:47:04Z

New page: '''Unreleased structure''' The entry 3vsd is ON HOLD Authors: Takashi Nakamura, Yoshito Kawai, Misumi Kataoka, Kazuhiko Ishikawa Description: Crystal Structure of the K127A Mutant of O...

New page

'''Unreleased structure'''

The entry 3vsd is ON HOLD

Authors: Takashi Nakamura, Yoshito Kawai, Misumi Kataoka, Kazuhiko Ishikawa

Description: Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine