Core autophagy machinery for autophagosome biogenesis

Autophagosomes form from a cup-shaped phagophore that grows around cytoplasmic cargo and closes into a double-membrane vesicle. Formation needs a conserved set of autophagy-related (Atg) proteins: the Atg1/ULK kinase with Atg13 starts assembly; the class III phosphatidylinositol 3-kinase complex (Vps34, Vps15, Atg6/Beclin and Atg14) marks the membrane with phosphatidylinositol 3-phosphate; Atg9 vesicles seed the membrane and the Atg2-Atg18/WIPI bridge feeds it lipid from the ER; and two ubiquitin-like conjugation systems link Atg12 to Atg5 and Atg8 to phosphatidylethanolamine. This module is the eukaryote-wide protein core, written so that it can be evaluated in any genome.

MODULE:autophagosome_core_biogenesisDRAFTCONCRETEBiological Processmodules/autophagosome_core_biogenesis.yaml
autophagosome assemblyGO:0000045

Eukaryote-wide scope: PAINT places nodes for Atg1/ULK, Vps34, Vps15, Atg6/Beclin, Atg9, Atg2, Atg7, Atg5, Atg12 and Atg8 at Eukaryota (taxon:2759). The Atg18/WIPI node carries no taxon and has seeds only from animals and budding yeast, so for that step the eukaryote-wide reach rests on the family entries table (yeast, Arabidopsis, Dictyostelium and human members). Each node is shown to be an ancestor of the human protein by its IBA rows or its IBD seeds. The Atg13, Atg3 and Atg4 families have no PAINT table locally, and their selectors rest on family membership. Read as a satisfiability rule, every non-optional part is expected in any eukaryote. Optional: Atg14, whose family is opisthokont-only in the local tables, and Atg16, whose family lacks the fungal protein. Molecular functions come from the human gene reviews' core functions; Atg7 carries one annoton for each conjugation arm, and Atg4 is typed from the human ATG4C review. Vps15 is untyped because its review records only a contribution to the Vps34 complex's kinase activity. Locations follow the human reviews' core-function locations: the phagophore assembly site for Atg1/ULK, Atg13, Vps34 and Atg2, the phagophore for Atg9, Atg14, Atg18/WIPI and the Atg12-Atg5-Atg16 complex, the cytosol for Atg7 and Atg3, the cytoplasm for Atg4 and the autophagosome membrane for Atg8. Two are inferred instead: Vps15 and Beclin are given the phagophore assembly site of their complex partner Vps34, because their own reviews do not record that location. Selector caveats are on each family: the Atg1/ULK and PROPPIN families over-match, and no Dictyostelium member is listed for Atg13 or Atg2. Not modelled: FIP200/Atg17 and ATG101, which have no local PANTHER entry for the human proteins and are not conserved as such across eukaryotes; Atg10, the E2 for Atg12 (no local entry for human ATG10); the Atg11 and receptor scaffolds of selective autophagy; and autophagosome closure and fusion with the lysosome or vacuole. The modules metazoan_autophagosome_biogenesis and phagophore_assembly_site describe the metazoan pathway and the yeast assembly site in more detail.

7Nodes
6Parts
0Variant Sets
0Variants
17Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:autophagosome_core_biogenesis 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.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • atg1_kinase_complex → pi3k_complex_i [NOT_CHECKED]
  • membrane_supply → atg_conjugation [NOT_CHECKED]

Function consistency and core coverage

17 gene-function check(s) reflected in core functions · 0 conflict(s) · 14 evidence or coverage gap(s) (34 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
atg1_ulk_kinase ULK1 (human)
UniProtKB:O75385
Family Representative 		protein serine/threonine kinase activity
GO:0004674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg13_regulator ATG13 (human)
UniProtKB:O75143
Family Representative 		protein kinase regulator activity
GO:0019887 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
vps34_kinase PIK3C3 (human)
UniProtKB:Q8NEB9
Family Representative 		1-phosphatidylinositol-3-kinase activity
GO:0016303 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg6_beclin BECN1 (human)
UniProtKB:Q14457
Family Representative 		protein-macromolecule adaptor activity
GO:0030674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg14_targeting ATG14 (human)
UniProtKB:Q6ZNE5
Family Representative 		protein-membrane adaptor activity
GO:0043495 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg9_scramblase ATG9A (human)
UniProtKB:Q7Z3C6
Family Representative 		phospholipid scramblase activity
GO:0017128 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg2_lipid_transfer ATG2A (human)
UniProtKB:Q2TAZ0
Family Representative 		lipid transfer activity
GO:0120013 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg18_wipi WIPI2 (human)
UniProtKB:Q9Y4P8
Family Representative 		phosphatidylinositol-3-phosphate binding
GO:0032266 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg7_e1 ATG7 (human)
UniProtKB:O95352
Family Representative 		Atg12 activating enzyme activity
GO:0019778 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg7_e1_atg8 ATG7 (human)
UniProtKB:O95352
Family Representative 		Atg8 activating enzyme activity
GO:0019779 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg12_ubl ATG12 (human)
UniProtKB:O94817
Family Representative 		protein tag activity
GO:0031386 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg5_e3 ATG5 (human)
UniProtKB:Q9H1Y0
Family Representative 		Atg8-family ligase activity
GO:0019776 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg3_e2 ATG3 (human)
UniProtKB:Q9NT62
Family Representative 		Atg8-family conjugating enzyme activity
GO:0141046 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg4_protease ATG4C (human)
UniProtKB:Q96DT6
Family Representative 		protein-phosphatidylethanolamide deconjugating activity
GO:0019786 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg4_protease ATG4B (human)
UniProtKB:Q9Y4P1
Family Representative 		protein-phosphatidylethanolamide deconjugating activity
GO:0019786 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
atg4_protease ATG4D (human)
UniProtKB:Q86TL0
Family Representative 		protein-phosphatidylethanolamide deconjugating activity
GO:0019786 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg8_lc3 MAP1LC3B (human)
UniProtKB:Q9GZQ8
Family Representative 		phosphatidylethanolamine binding
GO:0008429 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg16_complex ATG16L1 (human)
UniProtKB:Q676U5
Family Representative 		protein-membrane adaptor activity
GO:0043495 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg1_ulk_kinase Atg1/ULK kinase family
PANTHER:PTHR24348
Family 		protein serine/threonine kinase activity
GO:0004674 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR24348.
atg13_regulator Atg13 subfamily
PANTHER:PTHR13430:SF4
Family 		protein kinase regulator activity
GO:0019887 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR13430:SF4.
vps34_kinase Vps34 subfamily
PANTHER:PTHR10048:SF7
Family 		1-phosphatidylinositol-3-kinase activity
GO:0016303 		Family Supported
Family review supports GO:0016303 for PANTHER:PTHR10048:SF7. All three PI3K classes phosphorylate phosphatidylinositol at the 3-position: class III VPS34 (SF7, selected by the phosphoinositide_biosynthesis and phagosome_maturation modules, and its sole activity), the class II PI3Ks (SF28, SF29, SF30), and the class I catalytic subunits in vitro (SF107, SF33, SF34, SF35), whose PIK3CA and PIK3CD reviews keep the term. Not the type III PI4Ks. SF111 (C. elegans AGE-1, a class I catalytic subunit) is listed too; its review keeps the in vitro activity as non-core. For the class I subfamilies the scope records a measured in vitro activity, not the physiological one: in cells their main substrate is PI(4,5)P2. Read "safe" for those subfamilies with that caveat.
atg6_beclin Atg6/Beclin family
PANTHER:PTHR12768
Family 		protein-macromolecule adaptor activity
GO:0030674 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR12768.
atg14_targeting Atg14/Barkor family
PANTHER:PTHR13664
Family 		protein-membrane adaptor activity
GO:0043495 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR13664.
atg9_scramblase Atg9 family
PANTHER:PTHR13038
Family 		phospholipid scramblase activity
GO:0017128 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR13038.
atg2_lipid_transfer Atg2 family
PANTHER:PTHR13190
Family 		lipid transfer activity
GO:0120013 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR13190.
atg18_wipi PROPPIN (Atg18/WIPI) family
PANTHER:PTHR11227
Family 		phosphatidylinositol-3-phosphate binding
GO:0032266 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11227.
atg7_e1 Atg7 subfamily
PANTHER:PTHR10953:SF3
Family 		Atg12 activating enzyme activity
GO:0019778 		Family Supported
Family review supports GO:0019778 for PANTHER:PTHR10953:SF3. ATG12 activation is the specialization of the ATG7 subfamily SF3; other E1-like subfamilies activate different carriers.
atg7_e1_atg8 Atg7 subfamily
PANTHER:PTHR10953:SF3
Family 		Atg8 activating enzyme activity
GO:0019779 		Family Supported
Family review supports GO:0019779 for PANTHER:PTHR10953:SF3. ATG8-family activation is the second activity of the ATG7 subfamily SF3.
atg12_ubl Atg12 family
PANTHER:PTHR13385
Family 		protein tag activity
GO:0031386 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR13385.
atg5_e3 Atg5 family
PANTHER:PTHR13040
Family 		Atg8-family ligase activity
GO:0019776 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR13040.
atg3_e2 Atg3 subfamily
PANTHER:PTHR12866:SF2
Family 		Atg8-family conjugating enzyme activity
GO:0141046 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR12866:SF2.
atg4_protease Atg4 family
PANTHER:PTHR22624
Family 		protein-phosphatidylethanolamide deconjugating activity
GO:0019786 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR22624.
atg8_lc3 Atg8 family
PANTHER:PTHR10969
Family 		phosphatidylethanolamine binding
GO:0008429 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR10969.
atg16_complex Atg16-like family
PANTHER:PTHR19878
Family 		protein-membrane adaptor activity
GO:0043495 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR19878.

Gene-review completeness (17/18 grounded genes reviewed)

8 complete review(s) · 7 with deep research · 1 missing review · 10 reviewed but lacking deep research

Gene Review Complete Deep research
ATG12 O94817 ✓ 54/55 ✗
ATG13 O75143 ✓ ✓ ✗
ATG14 Q6ZNE5 ✓ 93/95 ✓
ATG16L1 Q676U5 ✓ ✓ ✗
ATG2A Q2TAZ0 ✓ 30/31 ✓
ATG3 Q9NT62 ✓ ✓ ✗
ATG4C Q96DT6 ✓ ✓ ✗
ATG4D Q86TL0 ✓ ✓ ✓
ATG5 Q9H1Y0 ✓ 88/90 ✓
ATG7 O95352 ✓ ✓ ✓
ATG9A Q7Z3C6 ✓ ✓ ✗
BECN1 Q14457 ✓ 189/191 ✓
MAP1LC3B Q9GZQ8 ✓ ✓ ✗
PIK3C3 Q8NEB9 ✓ 108/119 ✓
PIK3R4 Q99570 ✓ 64/66 ✗
ATG4B (human) Q9Y4P1 ✗ — —
ULK1 O75385 ✓ 137/139 ✗
WIPI2 Q9Y4P8 ✓ 43/45 ✗

Details

Context
EukaryotaNCBITaxon:2759
Core autophagy machinery for autophagosome biogenesisBiological Processautophagosome_core_biogenesis
autophagosome assemblyGO:0000045
Context
EukaryotaNCBITaxon:2759

Connections

The Atg1/ULK complex recruits and activates the PI3-kinase complex at the assembly site.
pi3k_complex_i -> membrane_supply Provides Input For
Phosphatidylinositol 3-phosphate recruits Atg18/WIPI and with it Atg2.
Atg18/WIPI recruits the Atg12-Atg5-Atg16 complex, which lipidates Atg8 on the growing membrane.
Part 1: initiation
Atg1/ULK kinase complexProtein Complexatg1_kinase_complex

Annotons

Atg1/ULK protein kinase
atg1_ulk_kinase
Participant: Family: Atg1/ULK kinase family
Family:
Atg1/ULK kinase familyPANTHER:PTHR24348 The family over-matches: besides Atg1/ULK1/ULK2 it holds human ULK3, budding yeast Ksp1 and Sks1 and further Arabidopsis kinases, which are not autophagy-initiating kinases. Human ULK1's subfamily SF19 holds only vertebrate ULK1, and yeast Atg1 sits in SF22 with Ksp1 and Sks1, so no subfamily separates the Atg1 orthologs either.
Representative Members: ULK1 (human)UniProtKB:O75385

Function

protein serine/threonine kinase activityGO:0004674

Locations

phagophore assembly siteGO:0000407

Serine/threonine kinase that starts phagophore formation: it assembles with Atg13 at the phagophore assembly site and phosphorylates downstream autophagy proteins.

file:genes/human/ULK1/ULK1-ai-review.yaml
Reviewed core function of human ULK1: protein serine/threonine kinase activity.
file:interpro/panther/PTHR24348/PTHR24348-paint.tsv
PAINT ancestral-node rows for this step's family.
Atg13 kinase regulatory subunit
atg13_regulator
Participant: Family: Atg13 subfamily
Family:
Atg13 subfamilyPANTHER:PTHR13430:SF4 SF4 lists budding and fission yeast, Arabidopsis and human members; no Dictyostelium member is listed, so genomes from that lineage may fail this step for want of a selector. The family has no PAINT table locally.
Representative Members: ATG13 (human)UniProtKB:O75143

Function

protein kinase regulator activityGO:0019887

Locations

phagophore assembly siteGO:0000407

HORMA-domain subunit that binds Atg1/ULK and recruits the kinase complex to the phagophore assembly site.

file:genes/human/ATG13/ATG13-ai-review.yaml
Reviewed core function of human ATG13: protein kinase regulator activity.
file:interpro/panther/PTHR13430/PTHR13430-entries.csv
PANTHER family membership table; no PAINT node with descent evidence for the human protein is available, so the selector rests on membership alone.
Part 2: PI3P production
Class III PI3-kinase complex IProtein Complexpi3k_complex_i

Annotons

Vps34 class III phosphatidylinositol 3-kinase
vps34_kinase
Participant: Family: Vps34 subfamily
Family:
Vps34 subfamilyPANTHER:PTHR10048:SF7 Subfamily of the PI3/PI4-kinase family; it lists yeast, Arabidopsis, Dictyostelium and human Vps34 and excludes the class I and II PI3-kinases.
Representative Members: PIK3C3 (human)UniProtKB:Q8NEB9

Function

1-phosphatidylinositol-3-kinase activityGO:0016303

Locations

phagophore assembly siteGO:0000407

Lipid kinase that makes phosphatidylinositol 3-phosphate on the phagophore membrane.

file:genes/human/PIK3C3/PIK3C3-ai-review.yaml
Reviewed core function of human PIK3C3: 1-phosphatidylinositol-3-kinase activity.
file:interpro/panther/PTHR10048/PTHR10048-paint.tsv
PAINT ancestral-node rows for this step's family.
Vps15 regulatory kinase subunit
vps15_regulator
Participant: Family: Vps15 family
Family:
Vps15 familyPANTHER:PTHR17583
Representative Members: PIK3R4 (human)UniProtKB:Q99570

Locations

phagophore assembly siteGO:0000407

Pseudokinase-like scaffold that anchors Vps34 to membranes and is required for its activity. It contributes to the complex's phosphatidylinositol 3-kinase activity rather than enabling it, and an annoton function would assert enabling, so the step is left untyped.

file:interpro/panther/PTHR17583/PTHR17583-paint.tsv
PAINT ancestral-node rows for this step's family.
Atg6/Beclin scaffold
atg6_beclin
Participant: Family: Atg6/Beclin family
Family:
Atg6/Beclin familyPANTHER:PTHR12768 The family holds only Atg6/Vps30 and the Beclins (human BECN1 and BECN2).
Representative Members: BECN1 (human)UniProtKB:Q14457

Function

protein-macromolecule adaptor activityGO:0030674

Locations

phagophore assembly siteGO:0000407

Coiled-coil scaffold that holds the Vps34-Vps15 core together with Atg14 or UVRAG.

file:genes/human/BECN1/BECN1-ai-review.yaml
Reviewed core function of human BECN1: protein-macromolecule adaptor activity.
file:interpro/panther/PTHR12768/PTHR12768-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 1: phagophore targeting (optional)
Atg14 subunitMolecular Functionatg14_subunit

Optional because the family entries table lists only fission yeast and animal members and the PAINT node is placed at Opisthokonta (taxon:33154); whether plants and other lineages have an Atg14 in another family has not been checked.

Annotons

Atg14 targeting subunit
atg14_targeting
Participant: Family: Atg14/Barkor family
Family:
Atg14/Barkor familyPANTHER:PTHR13664
Representative Members: ATG14 (human)UniProtKB:Q6ZNE5

Function

protein-membrane adaptor activityGO:0043495

Locations

phagophoreGO:0061908

Subunit that directs the Vps34 complex to the phagophore assembly site.

file:genes/human/ATG14/ATG14-ai-review.yaml
Reviewed core function of human ATG14: protein-membrane adaptor activity.
file:interpro/panther/PTHR13664/PTHR13664-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 3: membrane supply and expansion
Atg9 vesicles and the Atg2-Atg18 lipid bridgeModulemembrane_supply

Annotons

Atg9 lipid scramblase
atg9_scramblase
Participant: Family: Atg9 family
Family:
Atg9 familyPANTHER:PTHR13038
Representative Members: ATG9A (human)UniProtKB:Q7Z3C6

Function

phospholipid scramblase activityGO:0017128

Locations

phagophoreGO:0061908

Integral-membrane trimer, carried on small vesicles, that seeds the phagophore and equilibrates lipids between its leaflets.

file:genes/human/ATG9A/ATG9A-ai-review.yaml
Reviewed core function of human ATG9A: phospholipid scramblase activity.
file:interpro/panther/PTHR13038/PTHR13038-paint.tsv
PAINT ancestral-node rows for this step's family.
Atg2 bridge-like lipid transfer protein
atg2_lipid_transfer
Participant: Family: Atg2 family
Family:
Atg2 familyPANTHER:PTHR13190 The family lists yeast, Arabidopsis and human Atg2 but no Dictyostelium member, so genomes from that lineage may fail this step for want of a selector.
Representative Members: ATG2A (human)UniProtKB:Q2TAZ0

Function

lipid transfer activityGO:0120013

Locations

phagophore assembly siteGO:0000407

Rod-shaped protein that tethers the phagophore rim to the ER and channels lipids into the growing membrane.

file:genes/human/ATG2A/ATG2A-ai-review.yaml
Reviewed core function of human ATG2A: lipid transfer activity.
file:interpro/panther/PTHR13190/PTHR13190-paint.tsv
PAINT ancestral-node rows for this step's family.
Atg18/WIPI PI3P effector
atg18_wipi
Participant: Family: PROPPIN (Atg18/WIPI) family
Family:
PROPPIN (Atg18/WIPI) familyPANTHER:PTHR11227 The family is all PROPPINs, so it also takes in yeast Atg21 and Hsv2 and human WDR45/WDR45B; the selector is met by any of them. The local entries table records no subfamilies, so the PANTHER subfamily of human WIPI2 (SF27) cannot be checked for its lineage spread and is not used.
Representative Members: WIPI2 (human)UniProtKB:Q9Y4P8

Function

phosphatidylinositol-3-phosphate bindingGO:0032266

Locations

phagophoreGO:0061908

PROPPIN beta-propeller that binds phosphatidylinositol 3-phosphate on the phagophore and recruits Atg2 and the Atg16 complex.

file:genes/human/WIPI2/WIPI2-ai-review.yaml
Reviewed core function of human WIPI2: phosphatidylinositol-3-phosphate binding.
file:interpro/panther/PTHR11227/PTHR11227-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 4: ubiquitin-like conjugation
Atg12 and Atg8 conjugation systemsModuleatg_conjugation

Annotons

Atg7 E1-like activating enzyme (Atg12 arm)
atg7_e1
Participant: Family: Atg7 subfamily
Family:
Atg7 subfamilyPANTHER:PTHR10953:SF3 Subfamily of the ubiquitin-activating enzyme family; it lists yeast, Arabidopsis, Dictyostelium and human Atg7 and excludes the other E1s.
Representative Members: ATG7 (human)UniProtKB:O95352

Function

Atg12 activating enzyme activityGO:0019778

Locations

cytosolGO:0005829

E1-like enzyme that activates Atg12 for conjugation to Atg5.

file:genes/human/ATG7/ATG7-ai-review.yaml
Reviewed core function of human ATG7: Atg12 activating enzyme activity.
file:interpro/panther/PTHR10953/PTHR10953-paint.tsv
PAINT ancestral-node rows for this step's family.
Atg7 E1-like activating enzyme (Atg8 arm)
atg7_e1_atg8
Participant: Family: Atg7 subfamily
Family:
Atg7 subfamilyPANTHER:PTHR10953:SF3
Representative Members: ATG7 (human)UniProtKB:O95352

Function

Atg8 activating enzyme activityGO:0019779

Locations

cytosolGO:0005829

The same enzyme activating Atg8 for transfer to Atg3.

file:genes/human/ATG7/ATG7-ai-review.yaml
Reviewed core function of human ATG7: Atg8 activating enzyme activity.
file:interpro/panther/PTHR10953/PTHR10953-paint.tsv
PAINT ancestral-node rows for this step's family.
Atg12 ubiquitin-like protein
atg12_ubl
Participant: Family: Atg12 family
Family:
Atg12 familyPANTHER:PTHR13385
Representative Members: ATG12 (human)UniProtKB:O94817

Function

protein tag activityGO:0031386

Locations

phagophoreGO:0061908

Ubiquitin-like protein conjugated to Atg5.

file:genes/human/ATG12/ATG12-ai-review.yaml
Reviewed core function of human ATG12: protein tag activity.
file:interpro/panther/PTHR13385/PTHR13385-paint.tsv
PAINT ancestral-node rows for this step's family.
Atg5 conjugation partner
atg5_e3
Participant: Family: Atg5 family
Family:
Atg5 familyPANTHER:PTHR13040
Representative Members: ATG5 (human)UniProtKB:Q9H1Y0

Function

Atg8-family ligase activityGO:0019776

Locations

phagophoreGO:0061908

Acceptor of Atg12; the Atg12-Atg5 conjugate acts as the E3-like enzyme that transfers Atg8 to phosphatidylethanolamine.

file:genes/human/ATG5/ATG5-ai-review.yaml
Reviewed core function of human ATG5: Atg8-family ligase activity.
file:interpro/panther/PTHR13040/PTHR13040-paint.tsv
PAINT ancestral-node rows for this step's family.
Atg3 E2-like conjugating enzyme
atg3_e2
Participant: Family: Atg3 subfamily
Family:
Atg3 subfamilyPANTHER:PTHR12866:SF2 SF2 lists yeast, Arabidopsis, Dictyostelium, Plasmodium and human Atg3. The family also holds Atg10, the E2 for Atg12 (fungal SF5), which is not modelled: human ATG10 has no local PANTHER entry.
Representative Members: ATG3 (human)UniProtKB:Q9NT62

Function

Atg8-family conjugating enzyme activityGO:0141046

Locations

cytosolGO:0005829

E2-like enzyme that carries Atg8 from Atg7 and transfers it to phosphatidylethanolamine.

file:genes/human/ATG3/ATG3-ai-review.yaml
Reviewed core function of human ATG3: Atg8-family conjugating enzyme activity.
file:interpro/panther/PTHR12866/PTHR12866-entries.csv
PANTHER family membership table; no PAINT node with descent evidence for the human protein is available, so the selector rests on membership alone.
Atg4 cysteine protease
atg4_protease
Participant: Family: Atg4 family
Family:
Atg4 familyPANTHER:PTHR22624 The selector is the whole Atg4 family, which has no PAINT table locally. Its entries table lists yeast, Arabidopsis, Dictyostelium and human Atg4 proteins. The function comes from the human ATG4C review (the ATG4D review records the same delipidating activity); human ATG4B, the main Atg8 protease, has no review here.
Representative Members: ATG4C (human)UniProtKB:Q96DT6 ATG4B (human)UniProtKB:Q9Y4P1 ATG4D (human)UniProtKB:Q86TL0

Function

protein-phosphatidylethanolamide deconjugating activityGO:0019786

Locations

cytoplasmGO:0005737

Cysteine protease that exposes the C-terminal glycine of Atg8 for conjugation and later removes Atg8 from phosphatidylethanolamine.

file:genes/human/ATG4C/ATG4C-ai-review.yaml
Reviewed core function of human ATG4C: protein-phosphatidylethanolamide deconjugating activity.
file:interpro/panther/PTHR22624/PTHR22624-entries.csv
PANTHER family membership table; no PAINT node with descent evidence for the human protein is available, so the selector rests on membership alone.
Atg8/LC3/GABARAP ubiquitin-like protein
atg8_lc3
Participant: Family: Atg8 family
Family:
Atg8 familyPANTHER:PTHR10969 The family holds all Atg8 proteins: yeast Atg8 and the LC3 and GABARAP subfamilies. The local entries table records no subfamilies, so the family is the selector.
Representative Members: MAP1LC3B (human)UniProtKB:Q9GZQ8

Function

phosphatidylethanolamine bindingGO:0008429

Locations

autophagosome membraneGO:0000421

Ubiquitin-like protein lipidated onto phosphatidylethanolamine of the phagophore membrane, where it drives expansion and binds cargo receptors.

file:genes/human/MAP1LC3B/MAP1LC3B-ai-review.yaml
Reviewed core function of human MAP1LC3B: phosphatidylethanolamine binding.
file:interpro/panther/PTHR10969/PTHR10969-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 1: lipidation site (optional)
Atg16 subunitMolecular Functionatg16_subunit

Optional because the selector does not reach fungi: interpro/panther/PTHR19878/PTHR19878-entries.csv lists Arabidopsis, Dictyostelium and human Atg16 proteins but no yeast Atg16, which is a much smaller coiled-coil protein, so a fungal genome would fail the step for want of a selector rather than of the protein.

Annotons

Atg16 coiled-coil subunit
atg16_complex
Participant: Family: Atg16-like family
Family:
Atg16-like familyPANTHER:PTHR19878
Representative Members: ATG16L1 (human)UniProtKB:Q676U5

Function

protein-membrane adaptor activityGO:0043495

Locations

phagophoreGO:0061908

Binds Atg12-Atg5 and targets the conjugate to the phagophore, setting where Atg8 is lipidated.

file:genes/human/ATG16L1/ATG16L1-ai-review.yaml
Reviewed core function of human ATG16L1: protein-membrane adaptor activity.
file:interpro/panther/PTHR19878/PTHR19878-paint.tsv
PAINT ancestral-node rows for this step's family.