Glycosylation and related congenital defects (Homo sapiens)

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3419121563518, 3318, 333716, 43173Beta-1,4-galactosyltransferase-1-deficiency-CDG-IId (CDG-2d)Glucosidase-1-deficiency- CDG-IIb (CDG-2b)Pathological roleof MAGT1 related tomental retardationis questionable.37UDP-N-acetylalpha-D-glucosamine dolichyl beta-D-mannosyl phosphateDPAGT1GlcNAc-PP-Dol30.38dolichyl phosphateALG13beta-D-glucoseUDP2842532, 475EndoplasmicReticulumGolgiApparatusDolichyl phosphateGMPPBGDP30.34Man5-GlcNac2-PP-DolDPM25, 45Man8-GlcNac2-PP-DolMan7-GlcNac2-PP-DolMan6-GlcNac2-PP-DolMan9-GlcNac2-PP-DolGlc3Man9-GlcNac2-PP-DolGlc2Man9-GlcNac2-PP-DolGlcMan9-GlcNac2-PP-DolGlc2Man9-GlcNac2-ProtGlc3Man9-GlcNac2-ProtMan3-GlcNac4-ProtMan3-GlcNac3-ProtSia2Gal2Man3-GlcNac4-ProtGal2Man3-GlcNac4-ProtSiaGalMan3-GlcNac3-ProtGDP-mannoseDol-P-ManMannose 6-PhosphateMannose 1-phosphateFructose 6-phosphate23231, 230.13730.1430.153630.1630.630.330.1030.530.1030.3330.430.230.12430.3130.32522, 46, 49Mannosyltransferase-1-deficiency-CDG-IkMannosyltransferase-2-deficiency-CDG-Ii4, 44Steroid 5 alpha-reductase 2 deficiencyMannosyltransferase4-5-deficiency (ALG11-CDG-Ip)9, 38UDP-GlcNac:Dol-P-GlcNac-P-transferase deficiency - IjDolichol kinase deficiency - CDG - Im11, 29Man5GIcNAc2-PP-Dol25, 31Dolichol phosphateDolichol-PP30.398, 39, 4130.930.830.11Man3GIcNAc2-PP-Dol9, 48Man4GIcNAc2-PP-DolDolicholPolyprenol13, 2620Man2GIcNAc2PP-DolMevalonate30ManGlcNAc2-PP-Dol30.738GlcNAc2-PP-DolMannosyltransferase6 deficiency (CDG-Ic)10Mannosyltransferase 7-9 deficiency (CDG-II)14, 21dolichyl phosphatedolichyl beta-D-mannosyl phosphateGlucosyltransferase 2deficiency (CDG-Ih)Magnesium transporter 1deficiency (MAGT1-CDG)N-acetylglucosaminyltransferase 2deficiency (CDG-IIa)Oligosaccharyl-transferase-subunit-tusc-3-deficiency Glucosyltransferase-1-deficiency-CDG-Ic (CDG1c)Mannosyltransferase-8-deficiency-CDG-Ig (CDG-1g)Dol-P-Man utilization 1 deficiency (CDG-1f)GDP-Man:Dol-Pmannosyl-transferase-3 -deficiencyGDP-Man:Dol-P mannosyltransferase subunit 1 deficiency-CDG Ie (CDG-1e)Phosphomannomutase-2-deficiency- CDG-Ia (CDG-1a)Phosphomannose-isomerase-deficiency- CDG-Ib (CDG-1b)40ALG1427


Description

Glycosylation is the most common postranslational modification. Defects in this pathway lead to autosomal recessive disorders, called Congenital disorders of glycosylation (CDG). Up to date about 50 CDGs have been identified and more are expected to be discovered. This category of metabolic disorders can be divided into four basic groups depending on where the glycosylation process occurs on the molecule. The depicts pathway depicts the group of N-glycosylation. Generally, N-glycosylation processes spread over three cellular compartments - cytosol, endoplasmic reticulum and Golgi apparatus. The associated mortality rate in combination with the limited treatment options for CDG, points out the relevance for further investigations of this pathway. Disorders resulting from an enzyme defect are highlighted in pink. This pathway was inspired by Chapter 30 of the book of Blau (ISBN 3642403360 (978-3642403361)).

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Bibliography

View all...
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History

View all...
CompareRevisionActionTimeUserComment
107174view14:26, 17 September 2019MaintBotChEBI identifier normalization
104484view05:30, 29 May 2019EgonwHarmonized the OMIM href URL pattern.
104277view12:19, 15 May 2019Fehrhartremoved "." from title
104247view18:48, 11 May 2019EgonwRemoved the RHEA: prefix from the identifier.
104032view17:44, 25 April 2019IreneHemelModified description
103562view09:54, 15 March 2019EviSchoenmakerALG14 changed from GeneProduct to Protein
103536view10:21, 13 March 2019EviSchoenmakerAdded alternative abbreviations under comments for the diseases
103388view15:22, 25 February 2019EviSchoenmakerLayout change
103387view14:31, 25 February 2019DeSlRemoved weird signs in lit. ref, part 2
103386view14:26, 25 February 2019DeSlRemoved weird signs in lit. ref, part 1
103374view17:56, 24 February 2019EviSchoenmakerCorrected OMIM links
103346view13:04, 22 February 2019DeSlUpdated Rhea for reaction connected to 30.11 (was undirected), added lit.refs for disease and protein.
103316view09:11, 22 February 2019EviSchoenmakerChanged identifers to primary ones as indicated by Jenkins
103291view15:47, 21 February 2019L DupuisAddition of ALG14 gene modulation to ALG13 based on literature
103273view16:46, 20 February 2019EviSchoenmakerCorrection of Rhea's on left side
103269view11:03, 20 February 2019EviSchoenmakerCorrection and addition of identifiers as well as enzymes
103254view15:37, 18 February 2019EviSchoenmakerDescription of some enzymes
103240view09:36, 18 February 2019EviSchoenmakerCorrected location of first two diseases
103239view09:28, 18 February 2019EviSchoenmakerAddition of general reference, and adjustement of comment in 30.1
103237view09:11, 18 February 2019EviSchoenmakerOntology Term : 'N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminic acid dissimilation pathway' added !
103236view09:08, 18 February 2019EviSchoenmakerOntology Term : 'altered carbohydrate metabolic pathway' added !
103235view09:07, 18 February 2019EviSchoenmakerOntology Term : 'autosomal recessive disease' added !
103234view09:06, 18 February 2019EviSchoenmakerOntology Term : 'inherited metabolic disorder' added !
103232view09:02, 18 February 2019EviSchoenmakerModified description
103230view08:53, 18 February 2019EviSchoenmakerColor change of disease boxes
103216view14:49, 17 February 2019DeSlTyped alpha to avoid weird characters.
103215view14:48, 17 February 2019DeSlChanged arrows for diseases to graphical lines, small layout changes
103180view15:01, 15 February 2019BrittPietersModified description
103178view14:55, 15 February 2019BrittPietersAdded Rhea descriptions
103162view14:23, 15 February 2019EviSchoenmakerAdjusted arrows and boxes
103161view14:21, 15 February 2019EviSchoenmakerMore layout changes
103160view14:20, 15 February 2019EviSchoenmakerEnzyme label into number and general layout
103155view13:19, 15 February 2019EviSchoenmakerAddition of diseases to the right section
103146view09:43, 15 February 2019EviSchoenmakerAddition of diseases right part
103140view08:56, 15 February 2019EviSchoenmakerAdjusted failed literature annotation
103137view08:48, 15 February 2019DeSlAdded info for litref.
103131view14:14, 14 February 2019EviSchoenmakerFurther literature addition to the left part
103130view13:05, 14 February 2019EviSchoenmakerAddition of references to cytosolic part
103129view12:31, 14 February 2019EviSchoenmakerOntology Term : 'congenital disorder of glycosylation' added !
103128view12:29, 14 February 2019EviSchoenmakerModified description
103127view12:26, 14 February 2019EviSchoenmakerModified description
103123view17:46, 13 February 2019DeSlModified title
103122view17:42, 13 February 2019DeSlAnnotated top middle section.
103121view17:23, 13 February 2019DeSlAdded more IDs to middle section, untill 30.16
103120view17:06, 13 February 2019DeSlAdded IDs for middle part, bottom.
103118view15:55, 13 February 2019EviSchoenmakerCombined versions with some additions of PubMed IDs
103117view15:33, 13 February 2019DeSlAdded righthand side of PW drawing
103116view15:28, 13 February 2019EviSchoenmakerNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
30.10ProteinQ9H6U8 (Uniprot-TrEMBL) Aka ;mannosyltransferase 7-9
30.11ProteinQ2TAA5 (Uniprot-TrEMBL) GDP-Man:Man(3)GlcNAc(2)-PP- Dol alpha-1,2-mannosyltransferase
30.13ProteinQ10469 (Uniprot-TrEMBL)
  • AKA MGAT2; N-acetylglucosaminyltransferase 2
  • Function"Plays an essential role in protein N-glycosylation. Catalyzes the transfer of N-acetylglucosamine (GlcNAc) onto the free terminal mannose moiety in the core structure of the nascent N-linked glycan chain, giving rise to the second branch in complex glycans." [https://www.uniprot.org/uniprot/Q10469]
30.14ProteinQ13724 (Uniprot-TrEMBL)
  • AKA GCS1; Glucosidase 1
  • Function:"Cleaves the distal alpha 1,2-linked glucose residue from the Glc3Man9GlcNAc2 oligosaccharide precursor in a highly specific manner." [https://www.uniprot.org/uniprot/Q13724]
30.15ProteinQ13454 (Uniprot-TrEMBL) AKA TUSC3; oligosaccharyltransferase subunit tusc 3
30.16ProteinQ9H0U3 (Uniprot-TrEMBL) Aka MAGT1; magnesium transporter 1
30.1ProteinO15305 (Uniprot-TrEMBL) AKA PMM, phosphomannomutase 2
30.2ProteinP34949 (Uniprot-TrEMBL) AKA MPI, phosphomannose isomerase
30.31ProteinO60762 (Uniprot-TrEMBL) AKA DPM1, GDP-Man:Dol-P mannosyltransferase subunit 1
30.32ProteinQ9P2X0 (Uniprot-TrEMBL)
  • AKA DPM3, GDP-Man:Dol-P mannosyltransferase 3
  • "Stabilizer subunit of the dolichol-phosphate mannose (DPM) synthase complex; tethers catalytic subunit DPM1 to the ER" [https://www.uniprot.org/uniprot/Q9P2X0]
30.33ProteinO75352 (Uniprot-TrEMBL) AKA MPDU1; Dol-P-Man utilization 1
30.34ProteinP15291 (Uniprot-TrEMBL) AKA B4GALT1; beta-1,4-galactosyltransferase 1
30.38ProteinQ9UPQ8 (Uniprot-TrEMBL) Dolichol kinase
30.39 ProteinQ9H8P0 (Uniprot-TrEMBL) Known as polyprenol reductase, which catalyzes reduction of the alpha-isoprene subunit of polyprenol. But also known to have steroid dehydrogenase activity.
30.3ProteinQ9Y672 (Uniprot-TrEMBL) Aka ALG6; glucosyltransferase 1.
30.4ProteinQ92685 (Uniprot-TrEMBL)
  • AKA ALG3, mannosyltransferase 6
  • Function:"Adds the first Dol-P-Man derived mannose in an alpha-1,3 linkage to Man5GlcNAc2-PP-Dol" [https://www.uniprot.org/uniprot/Q92685]
30.5ProteinQ9BV10 (Uniprot-TrEMBL) AKA ALG12, Mannosyltransferase 8
30.6ProteinQ9BVK2 (Uniprot-TrEMBL) AKA ALG8; Glucosyltransferase 2
30.7ProteinQ9H553 (Uniprot-TrEMBL) Alpha-1,3/1,6- mannosyltransferase ALG2
30.8ProteinQ9H3H5 (Uniprot-TrEMBL) Also known as UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase, which transfers the hexosyl group
30.9ProteinQ9BT22 (Uniprot-TrEMBL)
  • Chitobiosyldiphosphodolichol beta-mannosyltransferase mediates the hexosyl group transfer.
  • In Blau Book known as Mannosyltransferase 1
ALG13ProteinQ9NP73 (Uniprot-TrEMBL)
  • Labelled in UniProt as Putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13.
  • Found manually through RHEA idnetifier. This enzyme was not indicated in the Blau Book, but it catalyzes this exact reaction.
ALG14Protein199857 (Entrez Gene) ALG14
DPAGT1ProteinQ9H3H5 (Uniprot-TrEMBL)
  • In UniProt described as UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase.
  • Found manually through RHEA identifier reaction. Not indicated in the Blau Book Chapter 30.
DPM2ProteinO94777 (Uniprot-TrEMBL)
Dol-P-ManMetaboliteCHEBI:58211 (ChEBI)
Dolichol phosphateMetaboliteCHEBI:57683 (ChEBI) In RHEA stated as dolichyl phosphate, and in this reaction it results in a -2 charge.
Dolichol-PPMetaboliteCHEBI:15750 (ChEBI) In CheBi known as Dolichol diphosphate
DolicholMetaboliteCHEBI:16091 (ChEBI) Full name in RHEA: di-trans,poly-cis-dolichol
Dolichyl phosphateMetaboliteCHEBI:57683 (ChEBI)
Fructose 6-phosphateMetaboliteCHEBI:61527 (ChEBI)
GDP-mannoseMetaboliteCHEBI:57527 (ChEBI)
GDPMetaboliteCHEBI:58189 (ChEBI)
GMPPBProteinQ9Y5P6 (Uniprot-TrEMBL) AKA mannose-1-phosphate guanylyltransferase [https://en.wikipedia.org/wiki/Mannose-1-phosphate_guanylyltransferase]
Gal2Man3-GlcNac4-ProtMetabolite
Glc2Man9-GlcNac2-PP-DolMetaboliteCHEBI:132522 (ChEBI)
Glc2Man9-GlcNac2-ProtMetaboliteCHEBI:59082 (ChEBI)
Glc3Man9-GlcNac2-PP-DolMetabolite
Glc3Man9-GlcNac2-ProtMetaboliteCHEBI:132537 (ChEBI)
GlcMan9-GlcNac2-PP-DolMetaboliteCHEBI:132521 (ChEBI)
GlcNAc-PP-DolMetaboliteCHEBI:58427 (ChEBI) In RHEA: N-acetyl-α-D-glucosaminyl-diphosphodolichol
GlcNAc2-PP-DolMetaboliteCHEBI:57269 (ChEBI) Aka N-acetylglucosamine
Man2GIcNAc2PP-DolMetaboliteCHEBI:132510 (ChEBI)
Man3-GlcNac3-ProtMetaboliteCHEBI:60615 (ChEBI)
Man3-GlcNac4-ProtMetaboliteCHEBI:60615 (ChEBI)
Man3GIcNAc2-PP-DolMetaboliteCHEBI:132511 (ChEBI)
Man4GIcNAc2-PP-DolMetabolite
Man5-GlcNac2-PP-DolMetaboliteCHEBI:132516 (ChEBI)
Man5GIcNAc2-PP-DolMetaboliteCHEBI:132515 (ChEBI)
Man6-GlcNac2-PP-DolMetabolite
Man7-GlcNac2-PP-DolMetaboliteCHEBI:132517 (ChEBI)
Man8-GlcNac2-PP-DolMetaboliteCHEBI:132519 (ChEBI)
Man9-GlcNac2-PP-DolMetaboliteCHEBI:132520 (ChEBI)
ManGlcNAc2-PP-Dol MetaboliteCHEBI:58472 (ChEBI)
Mannose 1-phosphateMetaboliteCHEBI:58409 (ChEBI)
Mannose 6-PhosphateMetaboliteCHEBI:58735 (ChEBI)
MevalonateMetaboliteCHEBI:17710 (ChEBI)
PolyprenolMetaboliteCHEBI:67132 (ChEBI) In RHEA and UniProt known as di-trans,cis-polyprenol.
Sia2Gal2Man3-GlcNac4-ProtMetabolite
SiaGalMan3-GlcNac3-ProtMetabolite
UDP-N-acetyl alpha-D-glucosamine MetaboliteCHEBI:57705 (ChEBI)
UDPMetaboliteCHEBI:58223 (ChEBI)
beta-D-glucoseMetaboliteCHEBI:15903 (ChEBI)
dolichyl

beta-D-mannosyl

phosphate
MetaboliteCHEBI:58211 (ChEBI)
dolichyl phosphateMetaboliteCHEBI:57683 (ChEBI)

Annotated Interactions

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SourceTargetTypeDatabase referenceComment
Dolichol-PPGlcNAc-PP-Dolmim-conversionRHEA:13290 (Rhea)
DolicholDolichol phosphatemim-conversionRHEA:13134 (Rhea)
Dolichyl phosphateRHEA:21185 (Rhea)
Fructose 6-phosphateMannose 6-Phosphatemim-conversionRHEA:12358 (Rhea)
GDP-mannoseDol-P-ManArrowRHEA:21185 (Rhea)
GDPmim-conversionRHEA:21185 (Rhea)
Glc3Man9-GlcNac2-ProtGlc2Man9-GlcNac2-Protmim-conversionRHEA:55989 (Rhea)
GlcMan9-GlcNac2-PP-DolGlc2Man9-GlcNac2-PP-Dolmim-conversionRHEA:31308 (Rhea)
GlcNAc-PP-DolGlcNAc2-PP-Dolmim-conversionRHEA:23381 (Rhea)
GlcNAc2-PP-DolManGlcNAc2-PP-Dol mim-conversionRHEA:13866 (Rhea)
Man3-GlcNac3-ProtMan3-GlcNac4-Protmim-conversionRHEA:12942 (Rhea)
Man3GIcNAc2-PP-DolMan4GIcNAc2-PP-Dolmim-conversionRHEA:29524 (Rhea)
Man4GIcNAc2-PP-DolMan5GIcNAc2-PP-Dolmim-conversionRHEA:29524 (Rhea)
Man5GIcNAc2-PP-DolMan5-GlcNac2-PP-Dolmim-conversionRHEA:29528 (Rhea)
Man7-GlcNac2-PP-DolMan8-GlcNac2-PP-Dolmim-conversionRHEA:29536 (Rhea)
Man8-GlcNac2-PP-DolMan9-GlcNac2-PP-Dolmim-conversionRHEA:29540 (Rhea)
Man9-GlcNac2-PP-DolGlcMan9-GlcNac2-PP-Dolmim-conversionRHEA:30636 (Rhea)
ManGlcNAc2-PP-Dol Man2GIcNAc2PP-Dolmim-conversionRHEA:29516 (Rhea)
Mannose 6-PhosphateMannose 1-phosphatemim-conversionRHEA:11142 (Rhea)
MevalonatePolyprenolmim-conversionRHEA:54384 (Rhea)
PolyprenolDolicholmim-conversionRHEA:34281 (Rhea)
UDP-N-acetyl alpha-D-glucosamine mim-conversionRHEA:12942 (Rhea)
UDPmim-conversionRHEA:12942 (Rhea)
beta-D-glucosemim-conversionRHEA:55989 (Rhea)
dolichyl

beta-D-mannosyl

phosphate
mim-conversionRHEA:29528 (Rhea)
dolichyl

beta-D-mannosyl

phosphate
mim-conversionRHEA:29540 (Rhea)
dolichyl phosphatemim-conversionRHEA:29528 (Rhea)
dolichyl phosphatemim-conversionRHEA:29540 (Rhea)
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