7o5z - Revision history

OCA at 12:45, 1 February 2024

OCA — Thu, 01 Feb 2024 12:45:20 GMT

←Older revision		Revision as of 12:45, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='7o5z' size='340' side='right'caption='[[7o5z]], [[Resolution\|resolution]] 2.07Å' scene=''>		<StructureSection load='7o5z' size='340' side='right'caption='[[7o5z]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7o5z]] is a 2 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=7O5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.07Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphomannomutase Phosphomannomutase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.8 5.4.2.8] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5z OCA], [https://pdbe.org/7o5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5z RCSB], [https://www.ebi.ac.uk/pdbsum/7o5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5z 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=7o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5z OCA], [https://pdbe.org/7o5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5z RCSB], [https://www.ebi.ac.uk/pdbsum/7o5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5z ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/PMM2_HUMAN PMM2_HUMAN]] Defects in PMM2 are the cause of congenital disorder of glycosylation type 1A (CDG1A) [MIM:[https://omim.org/entry/212065 212065]]; also known as carbohydrate-deficient glycoprotein syndrome type Ia (CDGS1A) or Jaeken syndrome. Congenital disorders of glycosylation are metabolic deficiencies in glycoprotein biosynthesis that usually cause severe mental and psychomotor retardation. They are characterized by under-glycosylated serum glycoproteins. CDG1A is an autosomal recessive disorder characterized by a severe encephalopathy with axial hypotonia, abnormal eye movement, and pronounced psychomotor retardation, as well as peripheral neuropathy, cerebellar hypoplasia, and retinitis pigmentosa. Patients show a peculiar distribution of subcutaneous fat, nipple retraction, and hypogonadism.<ref>PMID:9140401</ref> <ref>PMID:9497260</ref> <ref>PMID:9781039</ref> <ref>PMID:10066032</ref> <ref>PMID:10602363</ref> <ref>PMID:10571956</ref> <ref>PMID:11058895</ref> <ref>PMID:11058896</ref> <ref>PMID:10801058</ref> <ref>PMID:11350185</ref> <ref>PMID:12357336</ref> <ref>PMID:15844218</ref> <ref>PMID:17307006</ref>	+	[https://www.uniprot.org/uniprot/PMM2_HUMAN PMM2_HUMAN] Defects in PMM2 are the cause of congenital disorder of glycosylation type 1A (CDG1A) [MIM:[https://omim.org/entry/212065 212065]; also known as carbohydrate-deficient glycoprotein syndrome type Ia (CDGS1A) or Jaeken syndrome. Congenital disorders of glycosylation are metabolic deficiencies in glycoprotein biosynthesis that usually cause severe mental and psychomotor retardation. They are characterized by under-glycosylated serum glycoproteins. CDG1A is an autosomal recessive disorder characterized by a severe encephalopathy with axial hypotonia, abnormal eye movement, and pronounced psychomotor retardation, as well as peripheral neuropathy, cerebellar hypoplasia, and retinitis pigmentosa. Patients show a peculiar distribution of subcutaneous fat, nipple retraction, and hypogonadism.<ref>PMID:9140401</ref> <ref>PMID:9497260</ref> <ref>PMID:9781039</ref> <ref>PMID:10066032</ref> <ref>PMID:10602363</ref> <ref>PMID:10571956</ref> <ref>PMID:11058895</ref> <ref>PMID:11058896</ref> <ref>PMID:10801058</ref> <ref>PMID:11350185</ref> <ref>PMID:12357336</ref> <ref>PMID:15844218</ref> <ref>PMID:17307006</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PMM2_HUMAN PMM2_HUMAN]] Involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions (By similarity).	+	[https://www.uniprot.org/uniprot/PMM2_HUMAN PMM2_HUMAN] Involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 7o5z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7o5z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphomannomutase\|Phosphomannomutase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Phosphomannomutase]]~~	+	[[Category: Briso-Montiano A]]
-	[[Category: Briso-Montiano, A]]	+	[[Category: Del Cano-Ochoa F]]
-	[[Category: Cano-Ochoa, F ~~Del~~]]	+	[[Category: Perez B]]
-	[[Category: Perez, B]]	+	[[Category: Ramon-Maiques S]]
-	[[Category: Ramon-Maiques, S]]	+	[[Category: Rubio V]]
-	[[Category: Rubio, V]]	+	[[Category: Vilas A]]
-	[[Category: Vilas, A]]	+
-	~~[[Category: Congenital disorders of glycosylation]]~~	+
-	~~[[Category: Glycobiology]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Phosphomutase]]~~	+
-	~~[[Category: Phosphotransferase~~]]	+

OCA at 11:15, 30 March 2022

OCA — Wed, 30 Mar 2022 11:15:11 GMT

←Older revision		Revision as of 11:15, 30 March 2022
Line 1:		Line 1:

	==Human phosphomannomutase 2 (PMM2) with mutation T237M in apo state==		==Human phosphomannomutase 2 (PMM2) with mutation T237M in apo state==
-	<StructureSection load='7o5z' size='340' side='right'caption='[[7o5z]]' scene=''>	+	<StructureSection load='7o5z' size='340' side='right'caption='[[7o5z]], [[Resolution\|resolution]] 2.07Å' 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=7O5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5Z 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=7o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5z OCA], [https://pdbe.org/7o5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5z RCSB], [https://www.ebi.ac.uk/pdbsum/7o5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5z 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphomannomutase Phosphomannomutase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.8 5.4.2.8] </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=7o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5z OCA], [https://pdbe.org/7o5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5z RCSB], [https://www.ebi.ac.uk/pdbsum/7o5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5z ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[[https://www.uniprot.org/uniprot/PMM2_HUMAN PMM2_HUMAN]] Defects in PMM2 are the cause of congenital disorder of glycosylation type 1A (CDG1A) [MIM:[https://omim.org/entry/212065 212065]]; also known as carbohydrate-deficient glycoprotein syndrome type Ia (CDGS1A) or Jaeken syndrome. Congenital disorders of glycosylation are metabolic deficiencies in glycoprotein biosynthesis that usually cause severe mental and psychomotor retardation. They are characterized by under-glycosylated serum glycoproteins. CDG1A is an autosomal recessive disorder characterized by a severe encephalopathy with axial hypotonia, abnormal eye movement, and pronounced psychomotor retardation, as well as peripheral neuropathy, cerebellar hypoplasia, and retinitis pigmentosa. Patients show a peculiar distribution of subcutaneous fat, nipple retraction, and hypogonadism.<ref>PMID:9140401</ref> <ref>PMID:9497260</ref> <ref>PMID:9781039</ref> <ref>PMID:10066032</ref> <ref>PMID:10602363</ref> <ref>PMID:10571956</ref> <ref>PMID:11058895</ref> <ref>PMID:11058896</ref> <ref>PMID:10801058</ref> <ref>PMID:11350185</ref> <ref>PMID:12357336</ref> <ref>PMID:15844218</ref> <ref>PMID:17307006</ref>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PMM2_HUMAN PMM2_HUMAN]] Involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phosphomannomutase 2 (PMM2) deficiency, the most frequent congenital disorder of glycosylation (PMM2-CDG), is a severe condition, which has no cure. Due to the identification of destabilizing mutations, our group aims at increasing residual activity in PMM2-CDG patients, searching for pharmacochaperones. Detailed structural knowledge of hPMM2 might help identify variants amenable to pharmacochaperoning. hPMM2 structural information is limited to one incomplete structure deposited in the Protein Databank without associated publication, which lacked ligands and residues from a crucial loop. Here we report five complete crystal structures of hPMM2, three for wild-type and two for the p.Thr237Met variant frequently found among Spanish PMM2-CDG patients, free and bound to the essential activator glucose-1,6-bisphosphate (Glc-1,6-P2 ). In the hPMM2 homodimer, each subunit has a different conformation, reflecting movement of the distal core domain relative to the dimerization cap domain, supporting an opening/closing process during catalysis. Two Mg(2+) ions bind to the core domain, one catalytic and one structural. In the cap domain, the site for Glc-1,6-P2 is well delineated, while a Cl(-) ion binding at the intersubunit interface is predicted to strengthen dimerization. Patient-found amino acid substitutions are nonhomogeneously distributed throughout hPMM2, reflecting differential functional or structural importance for various parts of the protein. We classify 93 of 101 patient-reported single amino acid variants according to five potential pathogenetic mechanism affecting folding of the core and cap domains, linker 2 flexibility, dimerization, activator binding, and catalysis. We propose that ~80% and ~50% of the respective core and cap domains substitutions are potential candidates for pharmacochaperoning treatment.
		+
		+	Insight on molecular pathogenesis and pharmacochaperoning potential in phosphomannomutase 2 deficiency, provided by novel human phosphomannomutase 2 structures.,Briso-Montiano A, Del Cano-Ochoa F, Vilas A, Velazquez-Campoy A, Rubio V, Perez B, Ramon-Maiques S J Inherit Metab Dis. 2021 Dec 3. doi: 10.1002/jimd.12461. PMID:34859900<ref>PMID:34859900</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7o5z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Briso-Montiano A]]	+	[[Category: Phosphomannomutase]]
-	[[Category: ~~Del~~ Cano-Ochoa F]]	+	[[Category: Briso-Montiano, A]]
-	[[Category: Perez B]]	+	[[Category: Cano-Ochoa, F Del]]
-	[[Category: Ramon-Maiques S]]	+	[[Category: Perez, B]]
-	[[Category: Rubio V]]	+	[[Category: Ramon-Maiques, S]]
-	[[Category: Vilas A]]	+	[[Category: Rubio, V]]
		+	[[Category: Vilas, A]]
		+	[[Category: Congenital disorders of glycosylation]]
		+	[[Category: Glycobiology]]
		+	[[Category: Isomerase]]
		+	[[Category: Phosphomutase]]
		+	[[Category: Phosphotransferase]]

OCA at 07:00, 2 February 2022

OCA — Wed, 02 Feb 2022 07:00:50 GMT

←Older revision		Revision as of 07:00, 2 February 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7o5z is ~~ON HOLD until Paper Publication~~	+	==Human phosphomannomutase 2 (PMM2) with mutation T237M in apo state==
-		+	<StructureSection load='7o5z' size='340' side='right'caption='[[7o5z]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5Z FirstGlance]. <br>
-	~~Description~~:	+	</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=7o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5z OCA], [https://pdbe.org/7o5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5z RCSB], [https://www.ebi.ac.uk/pdbsum/7o5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5z ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Briso-Montiano A]]
		+	[[Category: Del Cano-Ochoa F]]
		+	[[Category: Perez B]]
		+	[[Category: Ramon-Maiques S]]
		+	[[Category: Rubio V]]
		+	[[Category: Vilas A]]

OCA: Protected "7o5z" [edit=sysop:move=sysop]

OCA — Wed, 21 Apr 2021 06:36:35 GMT

Protected "7o5z" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:36, 21 April 2021

OCA: New page: '''Unreleased structure''' The entry 7o5z is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 21 Apr 2021 06:36:33 GMT

New page: '''Unreleased structure''' The entry 7o5z is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7o5z is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]