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==Crystal structure of the N-acetylmannosamine kinase domain of human GNE protein==
==Crystal structure of the N-acetylmannosamine kinase domain of human GNE protein==
<StructureSection load='3eo3' size='340' side='right' caption='[[3eo3]], [[Resolution|resolution]] 2.84&Aring;' scene=''>
<StructureSection load='3eo3' size='340' side='right'caption='[[3eo3]], [[Resolution|resolution]] 2.84&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3eo3]] is a 3 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=3EO3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EO3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3eo3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EO3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EO3 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GNE, GLCNE ([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">GNE, GLCNE ([https://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=3eo3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eo3 OCA], [http://pdbe.org/3eo3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3eo3 RCSB], [http://www.ebi.ac.uk/pdbsum/3eo3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3eo3 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=3eo3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eo3 OCA], [https://pdbe.org/3eo3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eo3 RCSB], [https://www.ebi.ac.uk/pdbsum/3eo3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eo3 ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
== Disease ==
[[http://www.uniprot.org/uniprot/GLCNE_HUMAN GLCNE_HUMAN]] Defects in GNE are a cause of sialuria (SIALURIA) [MIM:[http://omim.org/entry/269921 269921]]; also known as sialuria French type. In sialuria, free sialic acid accumulates in the cytoplasm and gram quantities of neuraminic acid are secreted in the urine. The metabolic defect involves lack of feedback inhibition of UDP-GlcNAc 2-epimerase by CMP-Neu5Ac, resulting in constitutive overproduction of free Neu5Ac. Clinical features include variable degrees of developmental delay, coarse facial features and hepatomegaly. Sialuria inheritance is autosomal dominant.<ref>PMID:2808337</ref> <ref>PMID:10330343</ref> <ref>PMID:10356312</ref> <ref>PMID:11326336</ref>  Defects in GNE are the cause of inclusion body myopathy type 2 (IBM2) [MIM:[http://omim.org/entry/600737 600737]]. Hereditary inclusion body myopathies are a group of neuromuscular disorders characterized by adult onset, slowly progressive distal and proximal weakness and a typical muscle pathology including rimmed vacuoles and filamentous inclusions. IBM2 is an autosomal recessive disorder affecting mainly leg muscles, but with an unusual distribution that spares the quadriceps as also observed in Nonaka myopathy.<ref>PMID:11528398</ref> <ref>PMID:12409274</ref> <ref>PMID:12473769</ref> <ref>PMID:12473780</ref> <ref>PMID:12497639</ref> <ref>PMID:12811782</ref> <ref>PMID:15146476</ref>  Defects in GNE are the cause of Nonaka myopathy (NM) [MIM:[http://omim.org/entry/605820 605820]]; also known as distal myopathy with rimmed vacuoles (DMRV). NM is an autosomal recessive muscular disorder, allelic to inclusion body myopathy 2. It is characterized by weakness of the anterior compartment of the lower limbs with onset in early adulthood, and sparing of the quadriceps muscles. As the inclusion body myopathy, NM is histologically characterized by the presence of numerous rimmed vacuoles without inflammatory changes in muscle specimens.<ref>PMID:12325084</ref> <ref>PMID:11916006</ref> <ref>PMID:12177386</ref> <ref>PMID:12473753</ref> <ref>PMID:12913203</ref>   
[[https://www.uniprot.org/uniprot/GLCNE_HUMAN GLCNE_HUMAN]] Defects in GNE are a cause of sialuria (SIALURIA) [MIM:[https://omim.org/entry/269921 269921]]; also known as sialuria French type. In sialuria, free sialic acid accumulates in the cytoplasm and gram quantities of neuraminic acid are secreted in the urine. The metabolic defect involves lack of feedback inhibition of UDP-GlcNAc 2-epimerase by CMP-Neu5Ac, resulting in constitutive overproduction of free Neu5Ac. Clinical features include variable degrees of developmental delay, coarse facial features and hepatomegaly. Sialuria inheritance is autosomal dominant.<ref>PMID:2808337</ref> <ref>PMID:10330343</ref> <ref>PMID:10356312</ref> <ref>PMID:11326336</ref>  Defects in GNE are the cause of inclusion body myopathy type 2 (IBM2) [MIM:[https://omim.org/entry/600737 600737]]. Hereditary inclusion body myopathies are a group of neuromuscular disorders characterized by adult onset, slowly progressive distal and proximal weakness and a typical muscle pathology including rimmed vacuoles and filamentous inclusions. IBM2 is an autosomal recessive disorder affecting mainly leg muscles, but with an unusual distribution that spares the quadriceps as also observed in Nonaka myopathy.<ref>PMID:11528398</ref> <ref>PMID:12409274</ref> <ref>PMID:12473769</ref> <ref>PMID:12473780</ref> <ref>PMID:12497639</ref> <ref>PMID:12811782</ref> <ref>PMID:15146476</ref>  Defects in GNE are the cause of Nonaka myopathy (NM) [MIM:[https://omim.org/entry/605820 605820]]; also known as distal myopathy with rimmed vacuoles (DMRV). NM is an autosomal recessive muscular disorder, allelic to inclusion body myopathy 2. It is characterized by weakness of the anterior compartment of the lower limbs with onset in early adulthood, and sparing of the quadriceps muscles. As the inclusion body myopathy, NM is histologically characterized by the presence of numerous rimmed vacuoles without inflammatory changes in muscle specimens.<ref>PMID:12325084</ref> <ref>PMID:11916006</ref> <ref>PMID:12177386</ref> <ref>PMID:12473753</ref> <ref>PMID:12913203</ref>   
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/GLCNE_HUMAN GLCNE_HUMAN]] Regulates and initiates biosynthesis of N-acetylneuraminic acid (NeuAc), a precursor of sialic acids. Plays an essential role in early development (By similarity). Required for normal sialylation in hematopoietic cells. Sialylation is implicated in cell adhesion, signal transduction, tumorigenicity and metastatic behavior of malignant cells.<ref>PMID:10334995</ref>   
[[https://www.uniprot.org/uniprot/GLCNE_HUMAN GLCNE_HUMAN]] Regulates and initiates biosynthesis of N-acetylneuraminic acid (NeuAc), a precursor of sialic acids. Plays an essential role in early development (By similarity). Required for normal sialylation in hematopoietic cells. Sialylation is implicated in cell adhesion, signal transduction, tumorigenicity and metastatic behavior of malignant cells.<ref>PMID:10334995</ref>   
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eo/3eo3_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eo/3eo3_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 36: Line 36:
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Human]]
[[Category: Large Structures]]
[[Category: Arrowsmith, C H]]
[[Category: Arrowsmith, C H]]
[[Category: Bochkarev, A]]
[[Category: Bochkarev, A]]

Revision as of 12:11, 23 February 2022

Crystal structure of the N-acetylmannosamine kinase domain of human GNE proteinCrystal structure of the N-acetylmannosamine kinase domain of human GNE protein

Structural highlights

3eo3 is a 3 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
Gene:GNE, GLCNE (HUMAN)
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[GLCNE_HUMAN] Defects in GNE are a cause of sialuria (SIALURIA) [MIM:269921]; also known as sialuria French type. In sialuria, free sialic acid accumulates in the cytoplasm and gram quantities of neuraminic acid are secreted in the urine. The metabolic defect involves lack of feedback inhibition of UDP-GlcNAc 2-epimerase by CMP-Neu5Ac, resulting in constitutive overproduction of free Neu5Ac. Clinical features include variable degrees of developmental delay, coarse facial features and hepatomegaly. Sialuria inheritance is autosomal dominant.[1] [2] [3] [4] Defects in GNE are the cause of inclusion body myopathy type 2 (IBM2) [MIM:600737]. Hereditary inclusion body myopathies are a group of neuromuscular disorders characterized by adult onset, slowly progressive distal and proximal weakness and a typical muscle pathology including rimmed vacuoles and filamentous inclusions. IBM2 is an autosomal recessive disorder affecting mainly leg muscles, but with an unusual distribution that spares the quadriceps as also observed in Nonaka myopathy.[5] [6] [7] [8] [9] [10] [11] Defects in GNE are the cause of Nonaka myopathy (NM) [MIM:605820]; also known as distal myopathy with rimmed vacuoles (DMRV). NM is an autosomal recessive muscular disorder, allelic to inclusion body myopathy 2. It is characterized by weakness of the anterior compartment of the lower limbs with onset in early adulthood, and sparing of the quadriceps muscles. As the inclusion body myopathy, NM is histologically characterized by the presence of numerous rimmed vacuoles without inflammatory changes in muscle specimens.[12] [13] [14] [15] [16]

Function

[GLCNE_HUMAN] Regulates and initiates biosynthesis of N-acetylneuraminic acid (NeuAc), a precursor of sialic acids. Plays an essential role in early development (By similarity). Required for normal sialylation in hematopoietic cells. Sialylation is implicated in cell adhesion, signal transduction, tumorigenicity and metastatic behavior of malignant cells.[17]

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

BACKGROUND: UDP-GlcNAc 2-epimerase/ManNAc 6-kinase, GNE, is a bi-functional enzyme that plays a key role in sialic acid biosynthesis. Mutations of the GNE protein cause sialurea or autosomal recessive inclusion body myopathy/Nonaka myopathy. GNE is the only human protein that contains a kinase domain belonging to the ROK (repressor, ORF, kinase) family. PRINCIPAL FINDINGS: We solved the structure of the GNE kinase domain in the ligand-free state. The protein exists predominantly as a dimer in solution, with small populations of monomer and higher-order oligomer in equilibrium with the dimer. Crystal packing analysis reveals the existence of a crystallographic hexamer, and that the kinase domain dimerizes through the C-lobe subdomain. Mapping of disease-related missense mutations onto the kinase domain structure revealed that the mutation sites could be classified into four different groups based on the location - dimer interface, interlobar helices, protein surface, or within other secondary structural elements. CONCLUSIONS: The crystal structure of the kinase domain of GNE provides a structural basis for understanding disease-causing mutations and a model of hexameric wild type full length enzyme. ENHANCED VERSION: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

Crystal structure of the N-acetylmannosamine kinase domain of GNE.,Tong Y, Tempel W, Nedyalkova L, Mackenzie F, Park HW PLoS One. 2009 Oct 20;4(10):e7165. PMID:19841673[18]

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

References

  1. ↑ Weiss P, Tietze F, Gahl WA, Seppala R, Ashwell G. Identification of the metabolic defect in sialuria. J Biol Chem. 1989 Oct 25;264(30):17635-6. PMID:2808337
  2. ↑ Seppala R, Lehto VP, Gahl WA. Mutations in the human UDP-N-acetylglucosamine 2-epimerase gene define the disease sialuria and the allosteric site of the enzyme. Am J Hum Genet. 1999 Jun;64(6):1563-9. PMID:10330343 doi:S0002-9297(07)63658-1
  3. ↑ Ferreira H, Seppala R, Pinto R, Huizing M, Martins E, Braga AC, Gomes L, Krasnewich DM, Sa Miranda MC, Gahl WA. Sialuria in a Portuguese girl: clinical, biochemical, and molecular characteristics. Mol Genet Metab. 1999 Jun;67(2):131-7. PMID:10356312 doi:10.1006/mgme.1999.2852
  4. ↑ Leroy JG, Seppala R, Huizing M, Dacremont G, De Simpel H, Van Coster RN, Orvisky E, Krasnewich DM, Gahl WA. Dominant inheritance of sialuria, an inborn error of feedback inhibition. Am J Hum Genet. 2001 Jun;68(6):1419-27. Epub 2001 Apr 18. PMID:11326336 doi:10.1086/320598
  5. ↑ Eisenberg I, Avidan N, Potikha T, Hochner H, Chen M, Olender T, Barash M, Shemesh M, Sadeh M, Grabov-Nardini G, Shmilevich I, Friedmann A, Karpati G, Bradley WG, Baumbach L, Lancet D, Asher EB, Beckmann JS, Argov Z, Mitrani-Rosenbaum S. The UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase gene is mutated in recessive hereditary inclusion body myopathy. Nat Genet. 2001 Sep;29(1):83-7. PMID:11528398 doi:10.1038/ng718
  6. ↑ Darvish D, Vahedifar P, Huo Y. Four novel mutations associated with autosomal recessive inclusion body myopathy (MIM: 600737). Mol Genet Metab. 2002 Nov;77(3):252-6. PMID:12409274
  7. ↑ Vasconcelos OM, Raju R, Dalakas MC. GNE mutations in an American family with quadriceps-sparing IBM and lack of mutations in s-IBM. Neurology. 2002 Dec 10;59(11):1776-9. PMID:12473769
  8. ↑ Broccolini A, Pescatori M, D'Amico A, Sabino A, Silvestri G, Ricci E, Servidei S, Tonali PA, Mirabella M. An Italian family with autosomal recessive inclusion-body myopathy and mutations in the GNE gene. Neurology. 2002 Dec 10;59(11):1808-9. PMID:12473780
  9. ↑ Eisenberg I, Grabov-Nardini G, Hochner H, Korner M, Sadeh M, Bertorini T, Bushby K, Castellan C, Felice K, Mendell J, Merlini L, Shilling C, Wirguin I, Argov Z, Mitrani-Rosenbaum S. Mutations spectrum of GNE in hereditary inclusion body myopathy sparing the quadriceps. Hum Mutat. 2003 Jan;21(1):99. PMID:12497639 doi:10.1002/humu.9100
  10. ↑ Del Bo R, Baron P, Prelle A, Serafini M, Moggio M, Fonzo AD, Castagni M, Bresolin N, Comi GP. Novel missense mutation and large deletion of GNE gene in autosomal-recessive inclusion-body myopathy. Muscle Nerve. 2003 Jul;28(1):113-7. PMID:12811782 doi:10.1002/mus.10391
  11. ↑ Broccolini A, Ricci E, Cassandrini D, Gliubizzi C, Bruno C, Tonoli E, Silvestri G, Pescatori M, Rodolico C, Sinicropi S, Servidei S, Zara F, Minetti C, Tonali PA, Mirabella M. Novel GNE mutations in Italian families with autosomal recessive hereditary inclusion-body myopathy. Hum Mutat. 2004 Jun;23(6):632. PMID:15146476 doi:10.1002/humu.9252
  12. ↑ Arai A, Tanaka K, Ikeuchi T, Igarashi S, Kobayashi H, Asaka T, Date H, Saito M, Tanaka H, Kawasaki S, Uyama E, Mizusawa H, Fukuhara N, Tsuji S. A novel mutation in the GNE gene and a linkage disequilibrium in Japanese pedigrees. Ann Neurol. 2002 Oct;52(4):516-9. PMID:12325084 doi:10.1002/ana.10341
  13. ↑ Kayashima T, Matsuo H, Satoh A, Ohta T, Yoshiura K, Matsumoto N, Nakane Y, Niikawa N, Kishino T. Nonaka myopathy is caused by mutations in the UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase gene (GNE). J Hum Genet. 2002;47(2):77-9. PMID:11916006 doi:10.1007/s100380200004
  14. ↑ Tomimitsu H, Ishikawa K, Shimizu J, Ohkoshi N, Kanazawa I, Mizusawa H. Distal myopathy with rimmed vacuoles: novel mutations in the GNE gene. Neurology. 2002 Aug 13;59(3):451-4. PMID:12177386
  15. ↑ Nishino I, Noguchi S, Murayama K, Driss A, Sugie K, Oya Y, Nagata T, Chida K, Takahashi T, Takusa Y, Ohi T, Nishimiya J, Sunohara N, Ciafaloni E, Kawai M, Aoki M, Nonaka I. Distal myopathy with rimmed vacuoles is allelic to hereditary inclusion body myopathy. Neurology. 2002 Dec 10;59(11):1689-93. PMID:12473753
  16. ↑ Yabe I, Higashi T, Kikuchi S, Sasaki H, Fukazawa T, Yoshida K, Tashiro K. GNE mutations causing distal myopathy with rimmed vacuoles with inflammation. Neurology. 2003 Aug 12;61(3):384-6. PMID:12913203
  17. ↑ Keppler OT, Hinderlich S, Langner J, Schwartz-Albiez R, Reutter W, Pawlita M. UDP-GlcNAc 2-epimerase: a regulator of cell surface sialylation. Science. 1999 May 21;284(5418):1372-6. PMID:10334995
  18. ↑ Tong Y, Tempel W, Nedyalkova L, Mackenzie F, Park HW. Crystal structure of the N-acetylmannosamine kinase domain of GNE. PLoS One. 2009 Oct 20;4(10):e7165. PMID:19841673 doi:10.1371/journal.pone.0007165

3eo3, resolution 2.84Å

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