5x3f - Revision history

OCA at 07:53, 22 November 2023

OCA — Wed, 22 Nov 2023 07:53:34 GMT

←Older revision		Revision as of 07:53, 22 November 2023
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	==Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain==		==Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain==
-	<StructureSection load='5x3f' size='340' side='right' caption='[[5x3f]], [[Resolution\|resolution]] 3.38Å' scene=''>	+	<StructureSection load='5x3f' size='340' side='right'caption='[[5x3f]], [[Resolution\|resolution]] 3.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x3f]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X3F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X3F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x3f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12], [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X3F FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=TPO:PHOSPHOTHREONINE'>TPO</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]] 3.38Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>spa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1280~~ "~~Micrococcus aureus~~" ~~(Rosenbach 1884) Zopf 1885]), Prkaca, Pkaca ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Putrescine_aminotransferase Putrescine aminotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.82 2.6.1.82]~~ </~~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=5x3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3f OCA], [https://pdbe.org/5x3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x3f RCSB], [https://www.ebi.ac.uk/pdbsum/5x3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3f 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=5x3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3f OCA], [~~http~~://pdbe.org/5x3f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x3f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x3f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3f ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PAT_ECOLI PAT_ECOLI]] Catalyzes the aminotransferase reaction from putrescine to 2-oxoglutarate, leading to glutamate and 4-aminobutanal, which spontaneously cyclizes to form 1-pyrroline. Is also able to transaminate cadaverine and, in lower extent, spermidine, but not ornithine. Alpha-ketobutyrate and pyruvate can also act as amino acceptors, although much less efficiently.<ref>PMID:12617754</ref>	+	[https://www.uniprot.org/uniprot/SPA_STAAU SPA_STAAU] [https://www.uniprot.org/uniprot/PAT_ECOLI PAT_ECOLI] Catalyzes the aminotransferase reaction from putrescine to 2-oxoglutarate, leading to glutamate and 4-aminobutanal, which spontaneously cyclizes to form 1-pyrroline. Is also able to transaminate cadaverine and, in lower extent, spermidine, but not ornithine. Alpha-ketobutyrate and pyruvate can also act as amino acceptors, although much less efficiently.<ref>PMID:12617754</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Putrescine aminotransferase~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: ~~Kim, J H~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kwon, N Y~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Lee, H~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: ~~Lee, J H~~]]	+	[[Category: Kim JH]]
-	[[Category: ~~Lee, J O~~]]	+	[[Category: Kwon NY]]
-	[[Category: ~~Youn, S J~~]]	+	[[Category: Lee H]]
-	[[Category: ~~Lyase~~]]	+	[[Category: Lee JH]]
-	[[Category: ~~Synthetic protein~~]]	+	[[Category: Lee JO]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Youn SJ]]

OCA at 11:27, 6 November 2017

OCA — Mon, 06 Nov 2017 11:27:42 GMT

←Older revision		Revision as of 11:27, 6 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x3f is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain==
		+	<StructureSection load='5x3f' size='340' side='right' caption='[[5x3f]], [[Resolution\|resolution]] 3.38Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x3f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X3F FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), Prkaca, Pkaca ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Putrescine_aminotransferase Putrescine aminotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.82 2.6.1.82] </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=5x3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3f OCA], [http://pdbe.org/5x3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x3f RCSB], [http://www.ebi.ac.uk/pdbsum/5x3f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3f ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PAT_ECOLI PAT_ECOLI]] Catalyzes the aminotransferase reaction from putrescine to 2-oxoglutarate, leading to glutamate and 4-aminobutanal, which spontaneously cyclizes to form 1-pyrroline. Is also able to transaminate cadaverine and, in lower extent, spermidine, but not ornithine. Alpha-ketobutyrate and pyruvate can also act as amino acceptors, although much less efficiently.<ref>PMID:12617754</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Generating artificial protein assemblies with complex shapes requires a method for connecting protein components with stable and predictable structures. Currently available methods for creating rigid protein assemblies rely on either complicated calculations or extensive trial and error. We describe a simple and efficient method for connecting two proteins via a fused alpha helix that is formed by joining two preexisting helices into a single extended helix. Because the end-to-end ligation of helices does not guarantee the formation of a continuous helix, we superimposed 1-2 turns of pairs of connecting helices by using a molecular graphics program. Then, we chose amino acids from the two natural sequences that would stabilize the connecting helix. This "shared helix method" is highly efficient. All the designed proteins that could be produced in Escherichia coli were readily crystallized and had the expected fusion structures. To prove the usefulness of this method, we produced two novel repeat proteins by assembling several copies of natural or artificial proteins with alpha helices at both termini. Their crystal structures demonstrated the successful assembly of the repeating units with the intended curved shapes. We propose that this method could dramatically expand the available repertoire of natural repeat proteins.

-	~~Authors:~~ Youn~~, S.J.~~, Kwon~~, N.Y.~~, Lee~~, J.H.~~, Kim, J~~.H.~~, Lee, H., Lee~~, J~~.O.	+	Construction of novel repeat proteins with rigid and predictable structures using a shared helix method.,Youn SJ, Kwon NY, Lee JH, Kim JH, Choi J, Lee H, Lee JO Sci Rep. 2017 Jun 1;7(1):2595. doi: 10.1038/s41598-017-02803-z. PMID:28572639<ref>PMID:28572639</ref>

-	~~Description: Crystal structure~~ of the ~~YgjG~~-~~Protein A~~-~~Zpa963-PKA catalytic domain~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Youn, S.J~~]]	+	<div class="pdbe-citations 5x3f" style="background-color:#fffaf0;"></div>
-	[[Category: Kim, J.H]]	+	== References ==
-	[[Category: ~~Lee~~, ~~J.O~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Putrescine aminotransferase]]
		+	[[Category: Kim, J H]]
		+	[[Category: Kwon, N Y]]
	[[Category: Lee, H]]		[[Category: Lee, H]]
-	[[Category: Lee, J.H]]	+	[[Category: Lee, J H]]
-	[[Category: ~~Kwon~~, ~~N.Y~~]]	+	[[Category: Lee, J O]]
		+	[[Category: Youn, S J]]
		+	[[Category: Lyase]]
		+	[[Category: Synthetic protein]]
		+	[[Category: Transferase]]

OCA at 20:08, 15 March 2017

OCA — Wed, 15 Mar 2017 20:08:30 GMT

←Older revision		Revision as of 20:08, 15 March 2017
Line 7:		Line 7:
	Description: Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain		Description: Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kim, J.H]]
-	[[Category: Lee, J.H]]
	[[Category: Youn, S.J]]		[[Category: Youn, S.J]]
		+	[[Category: Kim, J.H]]
	[[Category: Lee, J.O]]		[[Category: Lee, J.O]]
	[[Category: Lee, H]]		[[Category: Lee, H]]
		+	[[Category: Lee, J.H]]
	[[Category: Kwon, N.Y]]		[[Category: Kwon, N.Y]]

OCA: Protected "5x3f" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:41:52 GMT

Protected "5x3f" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:41, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x3f is ON HOLD until Paper Publication Authors: Youn, S.J., Kwon, N.Y., Lee, J.H., Kim, J.H., Lee, H., Lee, J.O. Description: Crystal structure of...

OCA — Thu, 09 Mar 2017 15:41:50 GMT

New page: '''Unreleased structure''' The entry 5x3f is ON HOLD until Paper Publication Authors: Youn, S.J., Kwon, N.Y., Lee, J.H., Kim, J.H., Lee, H., Lee, J.O. Description: Crystal structure of...

New page

'''Unreleased structure'''

The entry 5x3f is ON HOLD until Paper Publication

Authors: Youn, S.J., Kwon, N.Y., Lee, J.H., Kim, J.H., Lee, H., Lee, J.O.

Description: Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain
[[Category: Unreleased Structures]]
[[Category: Kim, J.H]]
[[Category: Lee, J.H]]
[[Category: Youn, S.J]]
[[Category: Lee, J.O]]
[[Category: Lee, H]]
[[Category: Kwon, N.Y]]