4pvr - Revision history

OCA at 17:23, 20 September 2023

OCA — Wed, 20 Sep 2023 17:23:08 GMT

←Older revision		Revision as of 17:23, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4pvr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4gdv 4gdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PVR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pvr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4gdv 4gdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PVR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.75Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=4pvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pvr OCA], [https://pdbe.org/4pvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pvr RCSB], [https://www.ebi.ac.uk/pdbsum/4pvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pvr 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=4pvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pvr OCA], [https://pdbe.org/4pvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pvr RCSB], [https://www.ebi.ac.uk/pdbsum/4pvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pvr ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:33, 8 February 2023

OCA — Wed, 08 Feb 2023 07:33:31 GMT

←Older revision		Revision as of 07:33, 8 February 2023
Line 1:		Line 1:

	==Crystal structure of partially-cleaved human l-asparaginase protein in complex with l-aspartate==		==Crystal structure of partially-cleaved human l-asparaginase protein in complex with l-aspartate==
-	<StructureSection load='4pvr' size='340' side='right' caption='[[4pvr]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='4pvr' size='340' side='right'caption='[[4pvr]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4pvr]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4gdv 4gdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PVR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4PVR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4pvr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4gdv 4gdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PVR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pvp\|4pvp]], [[4pvq\|4pvq]], [[4pvs\|4pvs]]</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=4pvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pvr OCA], [https://pdbe.org/4pvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pvr RCSB], [https://www.ebi.ac.uk/pdbsum/4pvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pvr ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ALP, ASRGL1, CRASH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=4pvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pvr OCA], [~~http~~://pdbe.org/4pvr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4pvr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4pvr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4pvr ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ASGL1_HUMAN ASGL1_HUMAN]] Has both L-asparaginase and beta-aspartyl peptidase activity. May be involved in the production of L-aspartate, which can act as an excitatory neurotransmitter in some brain regions. Is highly active with L-Asp beta-methyl ester. Besides, has catalytic activity toward beta-aspartyl dipeptides and their methyl esters, including beta-L-Asp-L-Phe, beta-L-Asp-L-Phe methyl ester (aspartame), beta-L-Asp-L-Ala, beta-L-Asp-L-Leu and beta-L-Asp-L-Lys. Does not have aspartylglucosaminidase activity and is inactive toward GlcNAc-L-Asn. Likewise, has no activity toward glutamine.<ref>PMID:19839645</ref>	+	[https://www.uniprot.org/uniprot/ASGL1_HUMAN ASGL1_HUMAN] Has both L-asparaginase and beta-aspartyl peptidase activity. May be involved in the production of L-aspartate, which can act as an excitatory neurotransmitter in some brain regions. Is highly active with L-Asp beta-methyl ester. Besides, has catalytic activity toward beta-aspartyl dipeptides and their methyl esters, including beta-L-Asp-L-Phe, beta-L-Asp-L-Phe methyl ester (aspartame), beta-L-Asp-L-Ala, beta-L-Asp-L-Leu and beta-L-Asp-L-Lys. Does not have aspartylglucosaminidase activity and is inactive toward GlcNAc-L-Asn. Likewise, has no activity toward glutamine.<ref>PMID:19839645</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4pvr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4pvr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Asparaginase 3D structures\|Asparaginase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Lavie, A~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Nomme, J~~]]	+	[[Category: Lavie A]]
-	[[Category: ~~Homodimer]]~~	+	[[Category: Nomme J]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: L-asparagine]]~~	+
-	~~[[Category: Ntn enzyme~~]]	+

OCA at 19:34, 5 August 2016

OCA — Fri, 05 Aug 2016 19:34:50 GMT

←Older revision		Revision as of 19:34, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of partially-cleaved human l-asparaginase protein in complex with l-aspartate==		==Crystal structure of partially-cleaved human l-asparaginase protein in complex with l-aspartate==
	<StructureSection load='4pvr' size='340' side='right' caption='[[4pvr]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='4pvr' size='340' side='right' caption='[[4pvr]], [[Resolution\|resolution]] 1.75Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pvp\|4pvp]], [[4pvq\|4pvq]], [[4pvs\|4pvs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pvp\|4pvp]], [[4pvq\|4pvq]], [[4pvs\|4pvs]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ALP, ASRGL1, CRASH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ALP, ASRGL1, CRASH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4pvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pvr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pvr RCSB], [http://www.ebi.ac.uk/pdbsum/4pvr 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=4pvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pvr OCA], [http://pdbe.org/4pvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pvr RCSB], [http://www.ebi.ac.uk/pdbsum/4pvr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pvr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4pvr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:15, 25 December 2014

OCA — Thu, 25 Dec 2014 05:15:45 GMT

←Older revision		Revision as of 05:15, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4pvr\| PDB=4pvr \| SCENE= }}~~	+	==Crystal structure of partially-cleaved human l-asparaginase protein in complex with l-aspartate==
-	===Crystal structure of partially-cleaved human l-asparaginase protein in complex with l-aspartate===	+	<StructureSection load='4pvr' size='340' side='right' caption='[[4pvr]], [[Resolution\|resolution]] 1.75Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22861376}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4pvr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4gdv 4gdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PVR FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pvp\|4pvp]], [[4pvq\|4pvq]], [[4pvs\|4pvs]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ALP, ASRGL1, CRASH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4pvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pvr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pvr RCSB], [http://www.ebi.ac.uk/pdbsum/4pvr PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/ASGL1_HUMAN ASGL1_HUMAN]] Has both L-asparaginase and beta-aspartyl peptidase activity. May be involved in the production of L-aspartate, which can act as an excitatory neurotransmitter in some brain regions. Is highly active with L-Asp beta-methyl ester. Besides, has catalytic activity toward beta-aspartyl dipeptides and their methyl esters, including beta-L-Asp-L-Phe, beta-L-Asp-L-Phe methyl ester (aspartame), beta-L-Asp-L-Ala, beta-L-Asp-L-Leu and beta-L-Asp-L-Lys. Does not have aspartylglucosaminidase activity and is inactive toward GlcNAc-L-Asn. Likewise, has no activity toward glutamine.<ref>PMID:19839645</ref>		[[http://www.uniprot.org/uniprot/ASGL1_HUMAN ASGL1_HUMAN]] Has both L-asparaginase and beta-aspartyl peptidase activity. May be involved in the production of L-aspartate, which can act as an excitatory neurotransmitter in some brain regions. Is highly active with L-Asp beta-methyl ester. Besides, has catalytic activity toward beta-aspartyl dipeptides and their methyl esters, including beta-L-Asp-L-Phe, beta-L-Asp-L-Phe methyl ester (aspartame), beta-L-Asp-L-Ala, beta-L-Asp-L-Leu and beta-L-Asp-L-Lys. Does not have aspartylglucosaminidase activity and is inactive toward GlcNAc-L-Asn. Likewise, has no activity toward glutamine.<ref>PMID:19839645</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Asparaginases catalyze the hydrolysis of the amino acid asparagine to aspartate and ammonia. Bacterial asparaginases are used in cancer chemotherapy to deplete asparagine from the blood, because several hematological malignancies depend on extracellular asparagine for growth. To avoid the immune response against the bacterial enzymes, it would be beneficial to replace them with human asparaginases. However, unlike the bacterial asparaginases, the human enzymes have a millimolar K(m) value for asparagine, making them inefficient in depleting the amino acid from blood. To facilitate the development of human variants suitable for therapeutic use, we determined the structure of human l-asparaginase (hASNase3). This asparaginase is an N-terminal nucleophile (Ntn) family member that requires autocleavage between Gly167 and Thr168 to become catalytically competent. For most Ntn hydrolases, this autoproteolytic activation occurs efficiently. In contrast, hASNas3 is relatively stable in its uncleaved state, and this allowed us to observe the structure of the enzyme prior to cleavage. To determine the structure of the cleaved state, we exploited our discovery that the free amino acid glycine promotes complete cleavage of hASNase3. Both enzyme states were elucidated in the absence and presence of the product aspartate. Together, these structures provide insight into the conformational changes required for cleavage and the precise enzyme-substrate interactions. The new understanding of hASNase3 will serve to guide the design of variants that possess a decreased K(m) value for asparagine, making the human enzyme a suitable replacement for the bacterial asparaginases in cancer therapy.

-	~~==About this Structure==~~	+	Structures of Apo and Product-Bound Human l-Asparaginase: Insights into the Mechanism of Autoproteolysis and Substrate Hydrolysis.,Nomme J, Su Y, Konrad M, Lavie A Biochemistry. 2012 Aug 28;51(34):6816-26. Epub 2012 Aug 14. PMID:22861376<ref>PMID:22861376</ref>
-	~~[[4pvr]] is a 2 chain structure. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.~~ac.il/oca-bin/send~~-~~pdb?obs=1&id=4gdv 4gdv]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4PVR OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:022861376</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Lavie, A.]]	+	== References ==
-	[[Category: Nomme, J.]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Lavie, A]]
		+	[[Category: Nomme, J]]
	[[Category: Homodimer]]		[[Category: Homodimer]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: L-asparagine]]		[[Category: L-asparagine]]
	[[Category: Ntn enzyme]]		[[Category: Ntn enzyme]]

OCA: Protected "4pvr" [edit=sysop:move=sysop]

OCA — Wed, 26 Mar 2014 09:15:59 GMT

Protected "4pvr" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:15, 26 March 2014

OCA: New page: {{STRUCTURE_4pvr| PDB=4pvr | SCENE= }} ===Crystal structure of partially-cleaved human l-asparaginase protein in complex with l-aspartate=== {{ABSTRACT_PUBMED_22861376}} ==Function==...

OCA — Wed, 26 Mar 2014 09:15:57 GMT

New page: {{STRUCTURE_4pvr| PDB=4pvr | SCENE= }} ===Crystal structure of partially-cleaved human l-asparaginase protein in complex with l-aspartate=== {{ABSTRACT_PUBMED_22861376}} ==Function==...

New page

{{STRUCTURE_4pvr| PDB=4pvr | SCENE= }}
===Crystal structure of partially-cleaved human l-asparaginase protein in complex with l-aspartate===
{{ABSTRACT_PUBMED_22861376}}

==Function==
[[http://www.uniprot.org/uniprot/ASGL1_HUMAN ASGL1_HUMAN]] Has both L-asparaginase and beta-aspartyl peptidase activity. May be involved in the production of L-aspartate, which can act as an excitatory neurotransmitter in some brain regions. Is highly active with L-Asp beta-methyl ester. Besides, has catalytic activity toward beta-aspartyl dipeptides and their methyl esters, including beta-L-Asp-L-Phe, beta-L-Asp-L-Phe methyl ester (aspartame), beta-L-Asp-L-Ala, beta-L-Asp-L-Leu and beta-L-Asp-L-Lys. Does not have aspartylglucosaminidase activity and is inactive toward GlcNAc-L-Asn. Likewise, has no activity toward glutamine.<ref>PMID:19839645</ref>

==About this Structure==
[[4pvr]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4gdv 4gdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PVR OCA].

==Reference==
<ref group="xtra">PMID:022861376</ref><references group="xtra"/><references/>
[[Category: Lavie, A.]]
[[Category: Nomme, J.]]
[[Category: Homodimer]]
[[Category: Hydrolase]]
[[Category: L-asparagine]]
[[Category: Ntn enzyme]]