5kij - Revision history

OCA at 10:01, 27 September 2023

OCA — Wed, 27 Sep 2023 10:01:30 GMT

←Older revision		Revision as of 10:01, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5kij' size='340' side='right'caption='[[5kij]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='5kij' size='340' side='right'caption='[[5kij]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kij]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KIJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kij]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KIJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PS:3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE'>1PS</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=LA:LANTHANUM+(III)+ION'>LA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.649Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAN1B1, UNQ747/PRO1477 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PS:3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE'>1PS</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=LA:LANTHANUM+(III)+ION'>LA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannosyl-oligosaccharide_1,2-alpha-mannosidase Mannosyl-oligosaccharide 1,2-alpha-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.113 3.2.1.113] </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=5kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kij OCA], [https://pdbe.org/5kij PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kij RCSB], [https://www.ebi.ac.uk/pdbsum/5kij PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kij 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=5kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kij OCA], [~~http~~://pdbe.org/5kij PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kij RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kij PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kij ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/MA1B1_HUMAN MA1B1_HUMAN]] Defects in MAN1B1 are the cause of mental retardation autosomal recessive type 15 (MRT15) [MIM:[~~http~~://omim.org/entry/614202 614202]]. Mental retardation is characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period.<ref>PMID:21763484</ref>	+	[https://www.uniprot.org/uniprot/MA1B1_HUMAN MA1B1_HUMAN] Defects in MAN1B1 are the cause of mental retardation autosomal recessive type 15 (MRT15) [MIM:[https://omim.org/entry/614202 614202]. Mental retardation is characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period.<ref>PMID:21763484</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MA1B1_HUMAN MA1B1_HUMAN]] Involved in glycoprotein quality control targeting of misfolded glycoproteins for degradation. It primarily trims a single alpha-1,2-linked mannose residue from Man(9)GlcNAc(2) to produce Man(8)GlcNAc(2), but at high enzyme concentrations, as found in the ER quality control compartment (ERQC), it further trims the carbohydrates to Man(5-6)GlcNAc(2).<ref>PMID:12090241</ref> <ref>PMID:18003979</ref>	+	[https://www.uniprot.org/uniprot/MA1B1_HUMAN MA1B1_HUMAN] Involved in glycoprotein quality control targeting of misfolded glycoproteins for degradation. It primarily trims a single alpha-1,2-linked mannose residue from Man(9)GlcNAc(2) to produce Man(8)GlcNAc(2), but at high enzyme concentrations, as found in the ER quality control compartment (ERQC), it further trims the carbohydrates to Man(5-6)GlcNAc(2).<ref>PMID:12090241</ref> <ref>PMID:18003979</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Mannosyl-oligosaccharide 1,2-alpha-mannosidase]]~~	+	[[Category: Karaveg K]]
-	[[Category: Karaveg, K]]	+	[[Category: Moremen KW]]
-	[[Category: Moremen~~, K W~~]]	+	[[Category: Xiang Y]]
-	[[Category: Xiang, Y]]	+
-	~~[[Category: Alpha/alpha-barrel]]~~	+
-	~~[[Category: Cation replacement]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein-glycan interaction~~]]	+

OCA at 12:17, 25 December 2019

OCA — Wed, 25 Dec 2019 12:17:05 GMT

←Older revision		Revision as of 12:17, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase and Man9GlcNAc2-PA complex==		==Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase and Man9GlcNAc2-PA complex==
-	<StructureSection load='5kij' size='340' side='right' caption='[[5kij]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='5kij' size='340' side='right'caption='[[5kij]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kij]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KIJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kij]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KIJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PS:3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE'>1PS</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=LA:LANTHANUM+(III)+ION'>LA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PS:3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE'>1PS</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=LA:LANTHANUM+(III)+ION'>LA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAN1B1, UNQ747/PRO1477 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannosyl-oligosaccharide_1,2-alpha-mannosidase Mannosyl-oligosaccharide 1,2-alpha-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.113 3.2.1.113] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannosyl-oligosaccharide_1,2-alpha-mannosidase Mannosyl-oligosaccharide 1,2-alpha-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.113 3.2.1.113] </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=5kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kij OCA], [http://pdbe.org/5kij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kij RCSB], [http://www.ebi.ac.uk/pdbsum/5kij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kij 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=5kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kij OCA], [http://pdbe.org/5kij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kij RCSB], [http://www.ebi.ac.uk/pdbsum/5kij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kij ProSAT]</span></td></tr>
Line 21:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 5kij" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kij" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Mannosidase 3D structures\|Mannosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Mannosyl-oligosaccharide 1,2-alpha-mannosidase]]		[[Category: Mannosyl-oligosaccharide 1,2-alpha-mannosidase]]
	[[Category: Karaveg, K]]		[[Category: Karaveg, K]]

OCA at 12:48, 10 May 2017

OCA — Wed, 10 May 2017 12:48:50 GMT

←Older revision		Revision as of 12:48, 10 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kij is ~~ON HOLD~~	+	==Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase and Man9GlcNAc2-PA complex==
		+	<StructureSection load='5kij' size='340' side='right' caption='[[5kij]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kij]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KIJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PS:3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE'>1PS</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=LA:LANTHANUM+(III)+ION'>LA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannosyl-oligosaccharide_1,2-alpha-mannosidase Mannosyl-oligosaccharide 1,2-alpha-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.113 3.2.1.113] </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=5kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kij OCA], [http://pdbe.org/5kij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kij RCSB], [http://www.ebi.ac.uk/pdbsum/5kij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kij ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/MA1B1_HUMAN MA1B1_HUMAN]] Defects in MAN1B1 are the cause of mental retardation autosomal recessive type 15 (MRT15) [MIM:[http://omim.org/entry/614202 614202]]. Mental retardation is characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period.<ref>PMID:21763484</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MA1B1_HUMAN MA1B1_HUMAN]] Involved in glycoprotein quality control targeting of misfolded glycoproteins for degradation. It primarily trims a single alpha-1,2-linked mannose residue from Man(9)GlcNAc(2) to produce Man(8)GlcNAc(2), but at high enzyme concentrations, as found in the ER quality control compartment (ERQC), it further trims the carbohydrates to Man(5-6)GlcNAc(2).<ref>PMID:12090241</ref> <ref>PMID:18003979</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secreted glycoproteins. Multiple glycoside hydrolase family 47 (GH47) alpha-mannosidases, including endoplasmic reticulum (ER) alpha-mannosidase I (ERManI) and Golgi alpha-mannosidase IA (GMIA), are responsible for cleavage of terminal alpha1,2-linked mannose residues to produce uniquely trimmed oligomannose isomers that are necessary for ER glycoprotein quality control and glycan maturation. ERManI and GMIA have similar catalytic domain structures, but each enzyme cleaves distinct residues from tribranched oligomannose glycan substrates. The structural basis for branch-specific cleavage by ERManI and GMIA was explored by replacing an essential enzyme-bound Ca2+ ion with a lanthanum (La3+) ion. This ion swap led to enzyme inactivation while retaining high-affinity substrate interactions. Cocrystallization of La3+-bound enzymes with Man9GlcNAc2 substrate analogs revealed enzyme-substrate complexes with distinct modes of glycan branch insertion into the respective enzyme active-site clefts. Both enzymes had glycan interactions that extended across the entire glycan structure, but each enzyme engaged a different glycan branch and used different sets of glycan interactions. Additional mutagenesis and time-course studies of glycan cleavage probed the structural basis of enzyme specificity. The results provide insights into the enzyme catalytic mechanisms and reveal structural snapshots of the sequential glycan cleavage events. The data also indicate that full steric access to glycan substrates determines the efficiency of mannose-trimming reactions that control the conversion to complex-type structures in mammalian cells.

-	~~Authors~~:	+	Substrate recognition and catalysis by GH47 alpha-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway.,Xiang Y, Karaveg K, Moremen KW Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):E7890-E7899. Epub 2016 Nov 17. PMID:27856750<ref>PMID:27856750</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5kij" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Mannosyl-oligosaccharide 1,2-alpha-mannosidase]]
		+	[[Category: Karaveg, K]]
		+	[[Category: Moremen, K W]]
		+	[[Category: Xiang, Y]]
		+	[[Category: Alpha/alpha-barrel]]
		+	[[Category: Cation replacement]]
		+	[[Category: Hydrolase]]
		+	[[Category: Protein-glycan interaction]]

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

OCA — Thu, 23 Jun 2016 21:40:35 GMT

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

←Older revision

Revision as of 21:40, 23 June 2016

OCA: New page: '''Unreleased structure''' The entry 5kij is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 23 Jun 2016 21:40:34 GMT

New page: '''Unreleased structure''' The entry 5kij is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5kij is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]