7o5l - Revision history

OCA at 12:45, 1 February 2024

2024-02-01T12:45:06Z

←Older revision		Revision as of 12:45, 1 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7o5l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803_substr._Kazusa Synechocystis sp. PCC 6803 substr. Kazusa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5L FirstGlance]. <br>		<table><tr><td colspan='2'>[[7o5l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803_substr._Kazusa Synechocystis sp. PCC 6803 substr. Kazusa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</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]] 1.74Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</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=7o5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5l OCA], [https://pdbe.org/7o5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5l RCSB], [https://www.ebi.ac.uk/pdbsum/7o5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5l 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=7o5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5l OCA], [https://pdbe.org/7o5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5l RCSB], [https://www.ebi.ac.uk/pdbsum/7o5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SAHH_SYNY3 SAHH_SYNY3]] May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine.	+	[https://www.uniprot.org/uniprot/SAHH_SYNY3 SAHH_SYNY3] May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine.
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:23, 8 September 2022

2022-09-08T06:23:40Z

←Older revision		Revision as of 06:23, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7o5l' size='340' side='right'caption='[[7o5l]], [[Resolution\|resolution]] 1.74Å' scene=''>		<StructureSection load='7o5l' size='340' side='right'caption='[[7o5l]], [[Resolution\|resolution]] 1.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7o5l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7o5l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803_substr._Kazusa Synechocystis sp. PCC 6803 substr. Kazusa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenosylhomocysteinase Adenosylhomocysteinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.3.1.1 3.3.1.1] </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=7o5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5l OCA], [https://pdbe.org/7o5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5l RCSB], [https://www.ebi.ac.uk/pdbsum/7o5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5l 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=7o5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5l OCA], [https://pdbe.org/7o5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5l RCSB], [https://www.ebi.ac.uk/pdbsum/7o5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SAHH_SYNY3 SAHH_SYNY3]] May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine.	+	[[https://www.uniprot.org/uniprot/SAHH_SYNY3 SAHH_SYNY3]] May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The mesophilic cyanobacterium Synechocystis sp. PCC 6803 encodes an S-adenosyl-L-homocysteine hydrolase (SAHase) of archaeal origin in its genome. SAHases are essential enzymes involved in the regulation of cellular S-adenosyl-L-methionine (SAM)-dependent methylation reactions. They are usually active as homotetramers or, less commonly, as homodimers. A SAHase subunit is composed of two major domains: a cofactor (NAD(+))-binding domain and a substrate (S-adenosyl-L-homocysteine)-binding domain. These are connected by a hinge element that is also a coordination site for an alkali-metal cation that influences domain movement during the catalytic cycle. Typically, the highest activity and strongest substrate binding of bacterial SAHases are observed in the presence of K(+) ions. The SAHase from Synechocystis (SynSAHase) is an exception in this respect. Enzymatic and isothermal titration calorimetry studies demonstrated that in contrast to K(+)-dependent SAHases, the activity and ligand binding of SynSAHase are not affected by the presence of any particular alkali ion. Moreover, in contrast to other SAHases, the cyanobacterial enzyme is in an equilibrium of two distinct oligomeric states corresponding to its dimeric and tetrameric forms in solution. To explain these phenomena, crystal structures of SynSAHase were determined for the enzyme crystallized in the presence of adenosine (a reaction byproduct or substrate) and sodium or rubidium cations. The structural data confirm that while SynSAHase shares common structural features with other SAHases, no alkali metal is coordinated by the cyanobacterial enzyme as a result of a different organization of the macromolecular environment of the site that is normally supposed to coordinate the metal cation. This inspired the generation of SynSAHase mutants that bind alkali-metal cations analogously to K(+)-dependent SAHases, as confirmed by crystallographic studies. Structural comparisons of the crystal structure of SynSAHase with other experimental models of SAHases suggest a possible explanation for the occurrence of the cyanobacterial enzyme in the tetrameric state. On the other hand, the reason for the existence of SynSAHase in the dimeric state in solution remains elusive.	+
-		+
-	Biochemical and structural insights into an unusual, alkali-metal-independent S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803.,Malecki PH, Imiolczyk B, Barciszewski J, Czyrko-Horczak J, Sliwiak J, Gawel M, Wozniak K, Jaskolski M, Brzezinski K Acta Crystallogr D Struct Biol. 2022 Jul 1;78(Pt 7):865-882. doi:, 10.1107/S2059798322005605. Epub 2022 Jun 14. PMID:35775986<ref>PMID:35775986</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7o5l" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Adenosylhomocysteinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Barciszewski, J]]	+	[[Category: Synechocystis sp. PCC 6803 substr. Kazusa]]
-	[[Category: Brzezinski, K]]	+	[[Category: Barciszewski J]]
-	[[Category: Czyrko-Horczak, J]]	+	[[Category: Brzezinski K]]
-	[[Category: Imiolczyk, B]]	+	[[Category: Czyrko-Horczak J]]
-	[[Category: Malecki~~, P H]]~~	+	[[Category: Imiolczyk B]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Malecki PH]]
-	~~[[Category: Regulation of sam-dependent methylation reaction~~]]	+

OCA at 05:24, 13 July 2022

2022-07-13T05:24:26Z

←Older revision		Revision as of 05:24, 13 July 2022
Line 1:		Line 1:

	==Crystal structure of S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803 cocrystallized with adenosine in the presence of Rb+ cations==		==Crystal structure of S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803 cocrystallized with adenosine in the presence of Rb+ cations==
-	<StructureSection load='7o5l' size='340' side='right'caption='[[7o5l]]' scene=''>	+	<StructureSection load='7o5l' size='340' side='right'caption='[[7o5l]], [[Resolution\|resolution]] 1.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7o5l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5L FirstGlance]. <br>
-	</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=7o5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5l OCA], [https://pdbe.org/7o5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5l RCSB], [https://www.ebi.ac.uk/pdbsum/7o5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5l ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenosylhomocysteinase Adenosylhomocysteinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.3.1.1 3.3.1.1] </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=7o5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5l OCA], [https://pdbe.org/7o5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5l RCSB], [https://www.ebi.ac.uk/pdbsum/7o5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5l ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/SAHH_SYNY3 SAHH_SYNY3]] May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The mesophilic cyanobacterium Synechocystis sp. PCC 6803 encodes an S-adenosyl-L-homocysteine hydrolase (SAHase) of archaeal origin in its genome. SAHases are essential enzymes involved in the regulation of cellular S-adenosyl-L-methionine (SAM)-dependent methylation reactions. They are usually active as homotetramers or, less commonly, as homodimers. A SAHase subunit is composed of two major domains: a cofactor (NAD(+))-binding domain and a substrate (S-adenosyl-L-homocysteine)-binding domain. These are connected by a hinge element that is also a coordination site for an alkali-metal cation that influences domain movement during the catalytic cycle. Typically, the highest activity and strongest substrate binding of bacterial SAHases are observed in the presence of K(+) ions. The SAHase from Synechocystis (SynSAHase) is an exception in this respect. Enzymatic and isothermal titration calorimetry studies demonstrated that in contrast to K(+)-dependent SAHases, the activity and ligand binding of SynSAHase are not affected by the presence of any particular alkali ion. Moreover, in contrast to other SAHases, the cyanobacterial enzyme is in an equilibrium of two distinct oligomeric states corresponding to its dimeric and tetrameric forms in solution. To explain these phenomena, crystal structures of SynSAHase were determined for the enzyme crystallized in the presence of adenosine (a reaction byproduct or substrate) and sodium or rubidium cations. The structural data confirm that while SynSAHase shares common structural features with other SAHases, no alkali metal is coordinated by the cyanobacterial enzyme as a result of a different organization of the macromolecular environment of the site that is normally supposed to coordinate the metal cation. This inspired the generation of SynSAHase mutants that bind alkali-metal cations analogously to K(+)-dependent SAHases, as confirmed by crystallographic studies. Structural comparisons of the crystal structure of SynSAHase with other experimental models of SAHases suggest a possible explanation for the occurrence of the cyanobacterial enzyme in the tetrameric state. On the other hand, the reason for the existence of SynSAHase in the dimeric state in solution remains elusive.
		+
		+	Biochemical and structural insights into an unusual, alkali-metal-independent S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803.,Malecki PH, Imiolczyk B, Barciszewski J, Czyrko-Horczak J, Sliwiak J, Gawel M, Wozniak K, Jaskolski M, Brzezinski K Acta Crystallogr D Struct Biol. 2022 Jul 1;78(Pt 7):865-882. doi:, 10.1107/S2059798322005605. Epub 2022 Jun 14. PMID:35775986<ref>PMID:35775986</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7o5l" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Adenosylhomocysteinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Barciszewski J]]	+	[[Category: Barciszewski, J]]
-	[[Category: Brzezinski K]]	+	[[Category: Brzezinski, K]]
-	[[Category: Czyrko-Horczak J]]	+	[[Category: Czyrko-Horczak, J]]
-	[[Category: Imiolczyk B]]	+	[[Category: Imiolczyk, B]]
-	[[Category: Malecki PH]]	+	[[Category: Malecki, P H]]
		+	[[Category: Hydrolase]]
		+	[[Category: Regulation of sam-dependent methylation reaction]]

OCA at 02:54, 21 April 2022

2022-04-21T02:54:08Z

←Older revision		Revision as of 02:54, 21 April 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7o5l is ON HOLD until Paper Publication~~	+	==Crystal structure of S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803 cocrystallized with adenosine in the presence of Rb+ cations==
-		+	<StructureSection load='7o5l' size='340' side='right'caption='[[7o5l]]' scene=''>
-	~~Authors: Malecki, P.H., Imiolczyk, B., Barciszewski, J., Czyrko-Horczak, J., Brzezinski, K.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5L FirstGlance]. <br>
-	~~Description:~~ Crystal structure of S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803 cocrystallized with adenosine in the presence of Rb+ cations	+	</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=7o5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5l OCA], [https://pdbe.org/7o5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5l RCSB], [https://www.ebi.ac.uk/pdbsum/7o5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5l ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Brzezinski~~, K]]	+	__TOC__
-	[[Category: ~~Barciszewski, J~~]]	+	</StructureSection>
-	[[Category: ~~Imiolczyk, B~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Malecki, P.H~~]]	+	[[Category: Barciszewski J]]
-	[[Category: Czyrko-Horczak, J]]	+	[[Category: Brzezinski K]]
		+	[[Category: Czyrko-Horczak J]]
		+	[[Category: Imiolczyk B]]
		+	[[Category: Malecki PH]]

OCA at 06:36, 21 April 2021

2021-04-21T06:36:00Z

←Older revision		Revision as of 06:36, 21 April 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7o5l is ON HOLD	+	The entry 7o5l is ON HOLD until Paper Publication

	Authors: Malecki, P.H., Imiolczyk, B., Barciszewski, J., Czyrko-Horczak, J., Brzezinski, K.		Authors: Malecki, P.H., Imiolczyk, B., Barciszewski, J., Czyrko-Horczak, J., Brzezinski, K.

OCA: Protected "7o5l" [edit=sysop:move=sysop]

2021-04-14T05:51:46Z

Protected "7o5l" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:51, 14 April 2021

OCA: New page: '''Unreleased structure''' The entry 7o5l is ON HOLD Authors: Malecki, P.H., Imiolczyk, B., Barciszewski, J., Czyrko-Horczak, J., Brzezinski, K. Description: Crystal structure of S-ade...

2021-04-14T05:51:45Z

New page: '''Unreleased structure''' The entry 7o5l is ON HOLD Authors: Malecki, P.H., Imiolczyk, B., Barciszewski, J., Czyrko-Horczak, J., Brzezinski, K. Description: Crystal structure of S-ade...

New page

'''Unreleased structure'''

The entry 7o5l is ON HOLD

Authors: Malecki, P.H., Imiolczyk, B., Barciszewski, J., Czyrko-Horczak, J., Brzezinski, K.

Description: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803 cocrystallized with adenosine in the presence of Rb+ cations
[[Category: Unreleased Structures]]
[[Category: Brzezinski, K]]
[[Category: Barciszewski, J]]
[[Category: Imiolczyk, B]]
[[Category: Malecki, P.H]]
[[Category: Czyrko-Horczak, J]]