7p7x - Revision history

OCA at 13:02, 1 February 2024

OCA — Thu, 01 Feb 2024 13:02:03 GMT

←Older revision		Revision as of 13:02, 1 February 2024
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	<StructureSection load='7p7x' size='340' side='right'caption='[[7p7x]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='7p7x' size='340' side='right'caption='[[7p7x]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7p7x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Halh1 Halh1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P7X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7p7x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haliscomenobacter_hydrossis_DSM_1100 Haliscomenobacter hydrossis DSM 1100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P7X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Halhy_2446 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=760192 HALH1])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=7p7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p7x OCA], [https://pdbe.org/7p7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p7x RCSB], [https://www.ebi.ac.uk/pdbsum/7p7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p7x 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=7p7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p7x OCA], [https://pdbe.org/7p7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p7x RCSB], [https://www.ebi.ac.uk/pdbsum/7p7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p7x ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F4KWH0_HALH1 F4KWH0_HALH1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Halh1~~]]	+	[[Category: Haliscomenobacter hydrossis DSM 1100]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bakunova~~, A K~~]]	+	[[Category: Bakunova AK]]
-	[[Category: Bezsudnova~~, E Y~~]]	+	[[Category: Bezsudnova EY]]
-	[[Category: Boyko~~, K M~~]]	+	[[Category: Boyko KM]]
-	[[Category: Nikolaeva~~, A Y~~]]	+	[[Category: Nikolaeva AY]]
-	[[Category: Popov~~, V O~~]]	+	[[Category: Popov VO]]
-	[[Category: Rakitina~~, T V]]~~	+	[[Category: Rakitina TV]]
-	~~[[Category: Amino transferase]]~~	+
-	~~[[Category: D-amino acid]]~~	+
-	~~[[Category: Daat]]~~	+
-	~~[[Category: Plp]]~~	+
-	~~[[Category: Transaminase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:01, 10 November 2021

OCA — Wed, 10 Nov 2021 08:01:05 GMT

←Older revision		Revision as of 08:01, 10 November 2021
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-	==Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (holo form)==	+	==Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (holo form).==
	<StructureSection load='7p7x' size='340' side='right'caption='[[7p7x]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='7p7x' size='340' side='right'caption='[[7p7x]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 05:56, 6 October 2021

OCA — Wed, 06 Oct 2021 05:56:56 GMT

←Older revision		Revision as of 05:56, 6 October 2021
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	==Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (holo form)==		==Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (holo form)==
-	<StructureSection load='7p7x' size='340' side='right'caption='[[7p7x]]' scene=''>	+	<StructureSection load='7p7x' size='340' side='right'caption='[[7p7x]], [[Resolution\|resolution]] 2.00Å' 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=7P7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P7X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7p7x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halh1 Halh1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P7X 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=7p7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p7x OCA], [https://pdbe.org/7p7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p7x RCSB], [https://www.ebi.ac.uk/pdbsum/7p7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p7x 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Halhy_2446 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=760192 HALH1])</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=7p7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p7x OCA], [https://pdbe.org/7p7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p7x RCSB], [https://www.ebi.ac.uk/pdbsum/7p7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p7x ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Among industrially important pyridoxal-5'-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.
		+
		+	The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme.,Bakunova AK, Nikolaeva AY, Rakitina TV, Isaikina TY, Khrenova MG, Boyko KM, Popov VO, Bezsudnova EY Molecules. 2021 Aug 20;26(16). pii: molecules26165053. doi:, 10.3390/molecules26165053. PMID:34443642<ref>PMID:34443642</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7p7x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Halh1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bakunova AK]]	+	[[Category: Bakunova, A K]]
-	[[Category: Bezsudnova EY]]	+	[[Category: Bezsudnova, E Y]]
-	[[Category: Boyko KM]]	+	[[Category: Boyko, K M]]
-	[[Category: Nikolaeva AY]]	+	[[Category: Nikolaeva, A Y]]
-	[[Category: Popov VO]]	+	[[Category: Popov, V O]]
-	[[Category: Rakitina TV]]	+	[[Category: Rakitina, T V]]
		+	[[Category: Amino transferase]]
		+	[[Category: D-amino acid]]
		+	[[Category: Daat]]
		+	[[Category: Plp]]
		+	[[Category: Transaminase]]
		+	[[Category: Transferase]]

OCA: Protected "7p7x" [edit=sysop:move=sysop]

OCA — Wed, 28 Jul 2021 10:36:21 GMT

Protected "7p7x" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:36, 28 July 2021

OCA: New page: ==Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (holo form)== == Struct...

OCA — Wed, 28 Jul 2021 10:36:20 GMT

New page: ==Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (holo form)== <StructureSection load='7p7x' size='340' side='right'caption='7p7x' scene=''> == Struct...

New page

==Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (holo form)==
<StructureSection load='7p7x' size='340' side='right'caption='[[7p7x]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P7X 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=7p7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p7x OCA], [https://pdbe.org/7p7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p7x RCSB], [https://www.ebi.ac.uk/pdbsum/7p7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p7x ProSAT]</span></td></tr>
</table>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Bakunova AK]]
[[Category: Bezsudnova EY]]
[[Category: Boyko KM]]
[[Category: Nikolaeva AY]]
[[Category: Popov VO]]
[[Category: Rakitina TV]]