1z8d: Difference between revisions

Latest revision as of 07:05, 23 August 2023

Crystal Structure of Human Muscle Glycogen Phosphorylase a with AMP and Glucose

Structural highlights

1z8d 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 2.3Å
Ligands:	ADE, AMP, GLC, LLP, SEP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PYGM_HUMAN Defects in PYGM are the cause of glycogen storage disease type 5 (GSD5) [MIM:232600; also known as McArdle disease. GSD5 is a metabolic disorder resulting in myopathy characterized by exercise intolerance, cramps, muscle weakness and recurrent myoglobinuria.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13]

Function

PYGM_HUMAN Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.

Evolutionary Conservation

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

References

↑ Tsujino S, Shanske S, DiMauro S. Molecular genetic heterogeneity of myophosphorylase deficiency (McArdle's disease). N Engl J Med. 1993 Jul 22;329(4):241-5. PMID:8316268
↑ Tsujino S, Shanske S, Martinuzzi A, Heiman-Patterson T, DiMauro S. Two novel missense mutations (E654K, L396P) in Caucasian patients with myophosphorylase deficiency (McArdle's disease). Hum Mutat. 1995;6(3):276-7. PMID:8535454 doi:https://dx.doi.org/10.1002/humu.1380060318
↑ Tsujino S, Shanske S, Nonaka I, DiMauro S. The molecular genetic basis of myophosphorylase deficiency (McArdle's disease). Muscle Nerve. 1995;3:S23-7. PMID:7603523
↑ Vorgerd M, Kubisch C, Burwinkel B, Reichmann H, Mortier W, Tettenborn B, Pongratz D, Lindemuth R, Tegenthoff M, Malin JP, Kilimann MW. Mutation analysis in myophosphorylase deficiency (McArdle's disease). Ann Neurol. 1998 Mar;43(3):326-31. PMID:9506549 doi:10.1002/ana.410430310
↑ Gamez J, Fernandez R, Bruno C, Andreu AL, Cervera C, Navarro C, Schwartz S, Dimauro S. A new mutation in the regulatory domain of the myophosphorylase gene affecting protein dimer contact. Muscle Nerve. 1999 Aug;22(8):1136-8. PMID:10417800
↑ Andreu AL, Bruno C, Tamburino L, Gamez J, Shanske S, Cervera C, Navarro C, DiMauro S. A new mutation in the myophosphorylase gene (Asn684Tyr) in a Spanish patient with McArdle's disease. Neuromuscul Disord. 1999 May;9(3):171-3. PMID:10382911
↑ Rubio JC, Martin MA, Garcia A, Campos Y, Cabello A, Culebras JM, Arenas J. McArdle's disease associated with homozygosity for the missense mutation Gly204Ser of the myophosphorylase gene in a Spanish patient. Neuromuscul Disord. 1999 May;9(3):174-5. PMID:10382912
↑ Fernandez R, Navarro C, Andreu AL, Bruno C, Shanske S, Gamez J, Teijeira S, Hernandez I, Teijeiro A, Fernandez JM, Musumeci O, DiMauro S. A novel missense mutation (W797R) in the myophosphorylase gene in Spanish patients with McArdle disease. Arch Neurol. 2000 Feb;57(2):217-9. PMID:10681080
↑ Rubio JC, Martin MA, Campos Y, Auciello R, Cabello A, Arenas J. A missense mutation W797R in the myophosphorylase gene in a Spanish patient with McArdle's disease. Muscle Nerve. 2000 Jan;23(1):129-31. PMID:10590419
↑ Rubio JC, Martin MA, Campos Y, Cabello A, Arenas J. A missense mutation T487N in the myophosphorylase gene in a Spanish patient with McArdle's disease. Neuromuscul Disord. 2000 Feb;10(2):138-40. PMID:10714589
↑ Martin MA, Rubio JC, Campos Y, Ricoy JR, Cabello A, Arenas J. A homozygous missense mutation (A659D) in the myophosphorylase gene in a Spanish patient with McArdle's disease. Neuromuscul Disord. 2000 Aug;10(6):447-9. PMID:10899452
↑ Martin MA, Rubio JC, Buchbinder J, Fernandez-Hojas R, del Hoyo P, Teijeira S, Gamez J, Navarro C, Fernandez JM, Cabello A, Campos Y, Cervera C, Culebras JM, Andreu AL, Fletterick R, Arenas J. Molecular heterogeneity of myophosphorylase deficiency (McArdle's disease): a genotype-phenotype correlation study. Ann Neurol. 2001 Nov;50(5):574-81. PMID:11706962
↑ Bruno C, Lanzillo R, Biedi C, Iadicicco L, Minetti C, Santoro L. Two new mutations in the myophosphorylase gene in Italian patients with McArdle's disease. Neuromuscul Disord. 2002 Jun;12(5):498-500. PMID:12031624

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Tsujino S, Shanske S, DiMauro S. Molecular genetic heterogeneity of myophosphorylase deficiency (McArdle's disease). N Engl J Med. 1993 Jul 22;329(4):241-5. PMID:8316268

[2] Tsujino S, Shanske S, Martinuzzi A, Heiman-Patterson T, DiMauro S. Two novel missense mutations (E654K, L396P) in Caucasian patients with myophosphorylase deficiency (McArdle's disease). Hum Mutat. 1995;6(3):276-7. PMID:8535454 doi:https://dx.doi.org/10.1002/humu.1380060318

[3] Tsujino S, Shanske S, Nonaka I, DiMauro S. The molecular genetic basis of myophosphorylase deficiency (McArdle's disease). Muscle Nerve. 1995;3:S23-7. PMID:7603523

[4] Vorgerd M, Kubisch C, Burwinkel B, Reichmann H, Mortier W, Tettenborn B, Pongratz D, Lindemuth R, Tegenthoff M, Malin JP, Kilimann MW. Mutation analysis in myophosphorylase deficiency (McArdle's disease). Ann Neurol. 1998 Mar;43(3):326-31. PMID:9506549 doi:10.1002/ana.410430310

[5] Gamez J, Fernandez R, Bruno C, Andreu AL, Cervera C, Navarro C, Schwartz S, Dimauro S. A new mutation in the regulatory domain of the myophosphorylase gene affecting protein dimer contact. Muscle Nerve. 1999 Aug;22(8):1136-8. PMID:10417800

[6] Andreu AL, Bruno C, Tamburino L, Gamez J, Shanske S, Cervera C, Navarro C, DiMauro S. A new mutation in the myophosphorylase gene (Asn684Tyr) in a Spanish patient with McArdle's disease. Neuromuscul Disord. 1999 May;9(3):171-3. PMID:10382911

[7] Rubio JC, Martin MA, Garcia A, Campos Y, Cabello A, Culebras JM, Arenas J. McArdle's disease associated with homozygosity for the missense mutation Gly204Ser of the myophosphorylase gene in a Spanish patient. Neuromuscul Disord. 1999 May;9(3):174-5. PMID:10382912

[8] Fernandez R, Navarro C, Andreu AL, Bruno C, Shanske S, Gamez J, Teijeira S, Hernandez I, Teijeiro A, Fernandez JM, Musumeci O, DiMauro S. A novel missense mutation (W797R) in the myophosphorylase gene in Spanish patients with McArdle disease. Arch Neurol. 2000 Feb;57(2):217-9. PMID:10681080

[9] Rubio JC, Martin MA, Campos Y, Auciello R, Cabello A, Arenas J. A missense mutation W797R in the myophosphorylase gene in a Spanish patient with McArdle's disease. Muscle Nerve. 2000 Jan;23(1):129-31. PMID:10590419

[10] Rubio JC, Martin MA, Campos Y, Cabello A, Arenas J. A missense mutation T487N in the myophosphorylase gene in a Spanish patient with McArdle's disease. Neuromuscul Disord. 2000 Feb;10(2):138-40. PMID:10714589

[11] Martin MA, Rubio JC, Campos Y, Ricoy JR, Cabello A, Arenas J. A homozygous missense mutation (A659D) in the myophosphorylase gene in a Spanish patient with McArdle's disease. Neuromuscul Disord. 2000 Aug;10(6):447-9. PMID:10899452

[12] Martin MA, Rubio JC, Buchbinder J, Fernandez-Hojas R, del Hoyo P, Teijeira S, Gamez J, Navarro C, Fernandez JM, Cabello A, Campos Y, Cervera C, Culebras JM, Andreu AL, Fletterick R, Arenas J. Molecular heterogeneity of myophosphorylase deficiency (McArdle's disease): a genotype-phenotype correlation study. Ann Neurol. 2001 Nov;50(5):574-81. PMID:11706962

[13] Bruno C, Lanzillo R, Biedi C, Iadicicco L, Minetti C, Santoro L. Two new mutations in the myophosphorylase gene in Italian patients with McArdle's disease. Neuromuscul Disord. 2002 Jun;12(5):498-500. PMID:12031624

[1]

[2]

[3]

[4]

[5]

[6]

[7]

[8]

[9]

[10]

[11]

[12]

[13]

@@ Line 1: / Line 1: @@
-[[Image:1z8d.png|left|200px]]
-{{STRUCTURE_1z8d|  PDB=1z8d  |  SCENE=  }}
+==Crystal Structure of Human Muscle Glycogen Phosphorylase a with AMP and Glucose==
+<StructureSection load='1z8d' size='340' side='right'caption='[[1z8d]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-===Crystal Structure of Human Muscle Glycogen Phosphorylase a with AMP and Glucose===
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1z8d]] 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=1Z8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z8D FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-==About this Structure==
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
-[[1z8d]] is a 1 chain structure of [[Glycogen Phosphorylase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z8D OCA].
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1z8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z8d OCA], [https://pdbe.org/1z8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z8d RCSB], [https://www.ebi.ac.uk/pdbsum/1z8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z8d ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/PYGM_HUMAN PYGM_HUMAN] Defects in PYGM are the cause of glycogen storage disease type 5 (GSD5) [MIM:[https://omim.org/entry/232600 232600]; also known as McArdle disease. GSD5 is a metabolic disorder resulting in myopathy characterized by exercise intolerance, cramps, muscle weakness and recurrent myoglobinuria.<ref>PMID:8316268</ref> <ref>PMID:8535454</ref> <ref>PMID:7603523</ref> <ref>PMID:9506549</ref> <ref>PMID:10417800</ref> <ref>PMID:10382911</ref> <ref>PMID:10382912</ref> <ref>PMID:10681080</ref> <ref>PMID:10590419</ref> <ref>PMID:10714589</ref> <ref>PMID:10899452</ref> <ref>PMID:11706962</ref> <ref>PMID:12031624</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/PYGM_HUMAN PYGM_HUMAN] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z8/1z8d_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1z8d ConSurf].
+<div style="clear:both"></div>
 ==See Also==
-*[[Glycogen Phosphorylase|Glycogen Phosphorylase]]
+*[[Glycogen phosphorylase 3D structures|Glycogen phosphorylase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016523484</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Phosphorylase]]
+[[Category: Large Structures]]
-[[Category: Crowther, R L.]]
+[[Category: Crowther RL]]
-[[Category: Hong, L N.]]
+[[Category: Hong LN]]
-[[Category: Kammlott, R U.]]
+[[Category: Kammlott RU]]
-[[Category: Levin, W.]]
+[[Category: Levin W]]
-[[Category: Li, S.]]
+[[Category: Li S]]
-[[Category: Liu, C M.]]
+[[Category: Liu CM]]
-[[Category: Lucas-McGady, D.]]
+[[Category: Lucas-McGady D]]
-[[Category: Lukacs, C M.]]
+[[Category: Lukacs CM]]
-[[Category: Oikonomakos, N G.]]
+[[Category: Oikonomakos NG]]
-[[Category: Pietranico, S.]]
+[[Category: Pietranico S]]
-[[Category: Reik, L.]]
+[[Category: Reik L]]
-[[Category: Transferase]]

1z8d: Difference between revisions

Latest revision as of 07:05, 23 August 2023

Crystal Structure of Human Muscle Glycogen Phosphorylase a with AMP and Glucose

Structural highlights

Disease

Function

Evolutionary Conservation

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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