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2q4r

From Proteopedia

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Current revision

Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)

Structural highlights

2q4r is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.09Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PMM2_HUMAN Defects in PMM2 are the cause of congenital disorder of glycosylation type 1A (CDG1A) [MIM: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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13]

Function

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).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.

Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744^[14]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Matthijs G, Schollen E, Pardon E, Veiga-Da-Cunha M, Jaeken J, Cassiman JJ, Van Schaftingen E. Mutations in PMM2, a phosphomannomutase gene on chromosome 16p13, in carbohydrate-deficient glycoprotein type I syndrome (Jaeken syndrome). Nat Genet. 1997 May;16(1):88-92. PMID:9140401 doi:10.1038/ng0597-88
↑ Matthijs G, Schollen E, Van Schaftingen E, Cassiman JJ, Jaeken J. Lack of homozygotes for the most frequent disease allele in carbohydrate-deficient glycoprotein syndrome type 1A. Am J Hum Genet. 1998 Mar;62(3):542-50. PMID:9497260 doi:S0002-9297(07)63834-8
↑ Kjaergaard S, Skovby F, Schwartz M. Absence of homozygosity for predominant mutations in PMM2 in Danish patients with carbohydrate-deficient glycoprotein syndrome type 1. Eur J Hum Genet. 1998 Jul-Aug;6(4):331-6. PMID:9781039 doi:10.1038/sj.ejhg.5200194
↑ Kondo I, Mizugishi K, Yoneda Y, Hashimoto T, Kuwajima K, Yuasa I, Shigemoto K, Kuroda Y. Missense mutations in phosphomannomutase 2 gene in two Japanese families with carbohydrate-deficient glycoprotein syndrome type 1. Clin Genet. 1999 Jan;55(1):50-4. PMID:10066032
↑ Kjaergaard S, Skovby F, Schwartz M. Carbohydrate-deficient glycoprotein syndrome type 1A: expression and characterisation of wild type and mutant PMM2 in E. coli. Eur J Hum Genet. 1999 Dec;7(8):884-8. PMID:10602363 doi:10.1038/sj.ejhg.5200398
↑ Vuillaumier-Barrot S, Barnier A, Cuer M, Durand G, Grandchamp B, Seta N. Characterization of the 415G>A (E139K) PMM2 mutation in carbohydrate-deficient glycoprotein syndrome type Ia disrupting a splicing enhancer resulting in exon 5 skipping. Hum Mutat. 1999 Dec;14(6):543-4. PMID:10571956 doi:<543::AID-HUMU17>3.0.CO;2-S 10.1002/(SICI)1098-1004(199912)14:6<543::AID-HUMU17>3.0.CO;2-S
↑ Matthijs G, Schollen E, Bjursell C, Erlandson A, Freeze H, Imtiaz F, Kjaergaard S, Martinsson T, Schwartz M, Seta N, Vuillaumier-Barrot S, Westphal V, Winchester B. Mutations in PMM2 that cause congenital disorders of glycosylation, type Ia (CDG-Ia). Hum Mutat. 2000 Nov;16(5):386-94. PMID:11058895 doi:<386::AID-HUMU2>3.0.CO;2-Y 10.1002/1098-1004(200011)16:5<386::AID-HUMU2>3.0.CO;2-Y
↑ Bjursell C, Erlandson A, Nordling M, Nilsson S, Wahlstrom J, Stibler H, Kristiansson B, Martinsson T. PMM2 mutation spectrum, including 10 novel mutations, in a large CDG type 1A family material with a focus on Scandinavian families. Hum Mutat. 2000 Nov;16(5):395-400. PMID:11058896 doi:<395::AID-HUMU3>3.0.CO;2-T 10.1002/1098-1004(200011)16:5<395::AID-HUMU3>3.0.CO;2-T
↑ Imtiaz F, Worthington V, Champion M, Beesley C, Charlwood J, Clayton P, Keir G, Mian N, Winchester B. Genotypes and phenotypes of patients in the UK with carbohydrate-deficient glycoprotein syndrome type 1. J Inherit Metab Dis. 2000 Mar;23(2):162-74. PMID:10801058
↑ Westphal V, Enns GM, McCracken MF, Freeze HH. Functional analysis of novel mutations in a congenital disorder of glycosylation Ia patient with mixed Asian ancestry. Mol Genet Metab. 2001 May;73(1):71-6. PMID:11350185 doi:10.1006/mgme.2001.3174
↑ Schollen E, Martens K, Geuzens E, Matthijs G. DHPLC analysis as a platform for molecular diagnosis of congenital disorders of glycosylation (CDG). Eur J Hum Genet. 2002 Oct;10(10):643-8. PMID:12357336 doi:10.1038/sj.ejhg.5200858
↑ Le Bizec C, Vuillaumier-Barrot S, Barnier A, Dupre T, Durand G, Seta N. A new insight into PMM2 mutations in the French population. Hum Mutat. 2005 May;25(5):504-5. PMID:15844218 doi:10.1002/humu.9336
↑ Schollen E, Keldermans L, Foulquier F, Briones P, Chabas A, Sanchez-Valverde F, Adamowicz M, Pronicka E, Wevers R, Matthijs G. Characterization of two unusual truncating PMM2 mutations in two CDG-Ia patients. Mol Genet Metab. 2007 Apr;90(4):408-13. Epub 2007 Feb 16. PMID:17307006 doi:S1096-7192(07)00027-3
↑ Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:http://dx.doi.org/10.1016/j.str.2007.06.019

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 See Also
7 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q4r"

@@ Line 1: / Line 1: @@
 ==Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)==
-<StructureSection load='2q4r' size='340' side='right' caption='[[2q4r]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
+<StructureSection load='2q4r' size='340' side='right'caption='[[2q4r]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q4r]] 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=2Q4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q4R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q4r]] 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=2Q4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4R FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</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]] 2.09&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2amy|2amy]]</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=2q4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4r OCA], [https://pdbe.org/2q4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4r RCSB], [https://www.ebi.ac.uk/pdbsum/2q4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4r ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PMM2, HS.459855 ([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/Phosphomannomutase Phosphomannomutase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4r OCA], [http://pdbe.org/2q4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q4r RCSB], [http://www.ebi.ac.uk/pdbsum/2q4r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4r ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/PMM2_HUMAN PMM2_HUMAN]] Defects in PMM2 are the cause of congenital disorder of glycosylation type 1A (CDG1A) [MIM:[http://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 ==
-[[http://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).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 41: / Line 38: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Phosphomannomutase]]
+[[Category: Large Structures]]
-[[Category: Structural genomic]]
+[[Category: Kondrashov DA]]
-[[Category: Kondrashov, D A]]
+[[Category: Levin EJ]]
-[[Category: Levin, E J]]
+[[Category: Phillips Jr GN]]
-[[Category: Phillips, G N]]
+[[Category: Wesenberg GE]]
-[[Category: Wesenberg, G E]]
-[[Category: Bc008310]]
-[[Category: Carbohydrate-deficient glycoprotein syndrome]]
-[[Category: Cesg]]
-[[Category: Ensemble refinement]]
-[[Category: Had superfamily]]
-[[Category: Hs 313504]]
-[[Category: Hs 459855]]
-[[Category: Isomerase]]
-[[Category: Jaecken disease]]
-[[Category: Pfam pf03332]]
-[[Category: Phosphatase]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Refinement methodology development]]

2q4r

From Proteopedia

Current revision

Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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