Mannose 6-phosphate tagging of lysosomal hydrolases — Golgi GlcNAc-1-phosphotransferase (GNPTAB) and its retention factor LYSET

Newly synthesised soluble lysosomal acid hydrolases are sorted away from the secretory pathway by a mannose 6-phosphate (M6P) recognition marker on their N-glycans. In the cis-Golgi the GlcNAc-1-phosphotransferase complex (alpha2beta2gamma2; catalytic alpha/beta subunits encoded by GNPTAB, gamma by GNPTG) recognises a conformational protein determinant shared by lysosomal hydrolases and transfers GlcNAc-1-phosphate from UDP-GlcNAc to C6 hydroxyls of mannose residues of their high-mannose N-glycans. The Golgi membrane protein LYSET (TMEM251) binds the GlcNAc-1-phosphotransferase, stabilising it and supporting its site-1 protease activation and Golgi retention, and is required for M6P tagging. In the trans-Golgi network the uncovering enzyme NAGPA removes the covering GlcNAc to expose M6P, and the M6P receptors (cation-dependent M6PR and cation-independent IGF2R) bind the tagged hydrolases and deliver them to endosomes, from which the receptors recycle. Loss of GNPTAB causes mucolipidosis II (I-cell disease) and MLIII alpha/beta, GNPTG loss causes MLIII gamma, and LYSET deficiency causes a mucolipidosis-like disorder, all with hypersecretion of lysosomal enzymes and lysosomal storage.

MODULE:mannose_6_phosphate_lysosomal_targetingDRAFTBiological Processmodules/mannose_6_phosphate_lysosomal_targeting.yaml
N-glycan processing to lysosomeGO:0016256
GO:0016256
N-glycan processing to lysosome
The module is the GO process N-glycan processing to lysosome (GO:0016256): formation of the mannose 6-phosphate marker on lysosomal hydrolase N-glycans.
file:human/GNPTAB/GNPTAB-ai-review.yaml
GNPTAB gene review (human)
The phosphotransferase step (UniProtKB:Q3T906, GO:0003976, Golgi membrane) matches the completed human GNPTAB review.
file:human/LYSET/LYSET-ai-review.yaml
LYSET gene review (human)
The retention/stabilisation step (UniProtKB:Q8N6I4; GO:0050821 protein stabilization, GO:0007041 lysosomal transport; Golgi membrane) matches the completed human LYSET review.
3Nodes
2Parts
0Variant Sets
0Variants
2Annotons
1Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:mannose_6_phosphate_lysosomal_targeting deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

1 gene-function check(s) reflected in core functions · 0 conflict(s) · 1 evidence or coverage gap(s) (2 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
gnptab_activity GNPTAB (human)
UniProtKB:Q3T906
Family Representative
UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity
GO:0003976
Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gnptab_activity GlcNAc-1-phosphotransferase subunits alpha/beta
PANTHER:PTHR24045:SF0
Family
UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity
GO:0003976
Family Review Missing
No supported structured family review is available for PANTHER:PTHR24045:SF0.

Gene-review completeness (2/2 grounded genes reviewed)

2 complete review(s) · 1 with deep research · 0 missing review · 1 reviewed but lacking deep research

Gene Review Complete Deep research
GNPTAB Q3T906 ✓ ✓ ✓
LYSET Q8N6I4 ✓ ✓ ✗

Details

Context
Golgi membraneGO:0000139
Mannose 6-phosphate tagging of lysosomal hydrolasesBiological Processmannose_6_phosphate_lysosomal_targeting
N-glycan processing to lysosomeGO:0016256
Context
Golgi membraneGO:0000139

Grounded to the completed human reviews of GNPTAB (UniProtKB:Q3T906, GO:0003976) and LYSET (Q8N6I4). PANTHER subfamily ids are those in each representative's UniProt cross-references, with labels copied from interpro/panther/panther.obo. This module deliberately covers only the tagging (phosphotransferase) stage because the remaining members have no AIGR gene review yet: GNPTG (gamma subunit of the phosphotransferase; MLIII gamma), NAGPA (uncovering enzyme in the trans-Golgi network that removes the covering GlcNAc to expose M6P), and the M6P receptors M6PR (cation-dependent) and IGF2R (cation-independent) that sort tagged hydrolases from the TGN to endosomes. When those reviews exist they should be added as an uncovering part and a receptor sorting part. Site-1 protease (MBTPS1), which activates the alpha/beta precursor, is upstream activation context. Disorders: GNPTAB (mucolipidosis II alpha/beta, mucolipidosis III alpha/beta), GNPTG (mucolipidosis III gamma), LYSET (mucolipidosis-like lysosomal storage disorder).

Connections

lyset_step -> gnptab_step Positively Regulates
LYSET is required for GlcNAc-1-phosphotransferase stability, processing and Golgi retention, and hence for M6P tagging.
Part 1: GlcNAc-1-phosphate transfer to lysosomal hydrolase N-glycans
UDP-GlcNAc + lysosomal-enzyme high-mannose glycan to UMP + GlcNAc-1-P-mannose glycanReactiongnptab_step

Annotons

GNPTAB: GlcNAc-1-phosphotransferase alpha/beta subunits
gnptab_activity
Participant: Family: GlcNAc-1-phosphotransferase subunits alpha/beta
Family:
GlcNAc-1-phosphotransferase subunits alpha/betaPANTHER:PTHR24045:SF0
Representative Members: GNPTAB (human)UniProtKB:Q3T906

Function

UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activityGO:0003976
Substrates: UDP-N-acetylglucosamine high-mannose N-glycan of a lysosomal hydrolase
Products: N-acetylglucosamine-1-phospho-mannose N-glycan UMP

Processes

N-glycan processing to lysosomeGO:0016256

Locations

Golgi membraneGO:0000139

Catalytic core of the alpha2beta2gamma2 complex; the alpha/beta precursor is activated by site-1 protease cleavage. Substrate recognition relies on a protein determinant of the hydrolases, with the GNPTG gamma subunit enhancing phosphorylation of a subset of them.

Part 2: Golgi retention and stabilisation of the phosphotransferase
LYSET binds and retains GlcNAc-1-phosphotransferase in the GolgiRegulatory Steplyset_step

Annotons

LYSET (TMEM251): lysosomal enzyme trafficking factor
lyset_role
Participant: Family: Lysosomal enzyme trafficking factor
Family:
Lysosomal enzyme trafficking factorPANTHER:PTHR31925:SF1
Representative Members: LYSET (human)UniProtKB:Q8N6I4

Processes

protein stabilizationGO:0050821 lysosomal transportGO:0007041

Locations

Golgi membraneGO:0000139

Small Golgi membrane protein that binds GNPTAB, stabilising it and supporting its site-1 protease cleavage, activity and Golgi retention; without LYSET the complex is lost to lysosomes and hydrolases are secreted. No specific molecular-function term is asserted (the LYSET review records none).