MLP3B_RAT
ID MLP3B_RAT Reviewed; 142 AA.
AC Q62625; Q6XVN7;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=Microtubule-associated proteins 1A/1B light chain 3B {ECO:0000305};
DE AltName: Full=Autophagy-related protein LC3 B;
DE AltName: Full=Autophagy-related ubiquitin-like modifier LC3 B;
DE AltName: Full=MAP1 light chain 3-like protein 2;
DE AltName: Full=MAP1A/MAP1B light chain 3 B;
DE Short=MAP1A/MAP1B LC3 B;
DE AltName: Full=Microtubule-associated protein 1 light chain 3 beta;
DE Flags: Precursor;
GN Name=Map1lc3b {ECO:0000312|RGD:621315}; Synonyms=Map1alc3, Map1lc3;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBUNIT, AND TISSUE SPECIFICITY.
RC TISSUE=Brain;
RX PubMed=7908909; DOI=10.1016/s0021-9258(19)78150-2;
RA Mann S.S., Hammarback J.A.;
RT "Molecular characterization of light chain 3. A microtubule binding subunit
RT of MAP1A and MAP1B.";
RL J. Biol. Chem. 269:11492-11497(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
RC STRAIN=Sprague-Dawley; TISSUE=Brain;
RA Dang Y., Yu L., Wu J., Pei Y.;
RT "Cloning and characterization of rat lc3 orthologs.";
RL Submitted (DEC-2002) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
RC STRAIN=Sprague-Dawley;
RA Zhou G., Dai F., Yu L.;
RT "Rattus norvegicus microtubule-associated protein 1 light chain 3
RT (Map1lc3).";
RL Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Heart, and Pituitary;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP PROTEIN SEQUENCE OF 31-37, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=Sprague-Dawley; TISSUE=Brain;
RA Lubec G., Kang S.U.;
RL Submitted (JUL-2007) to UniProtKB.
RN [6]
RP SUBCELLULAR LOCATION, CLEAVAGE, AND MUTAGENESIS OF GLY-120.
RX PubMed=11060023; DOI=10.1093/emboj/19.21.5720;
RA Kabeya Y., Mizushima N., Ueno T., Yamamoto A., Kirisako T., Noda T.,
RA Kominami E., Ohsumi Y., Yoshimori T.;
RT "LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome
RT membranes after processing.";
RL EMBO J. 19:5720-5728(2000).
RN [7]
RP REVIEW.
RX PubMed=15325588; DOI=10.1016/j.biocel.2004.05.009;
RA Tanida I., Ueno T., Kominami E.;
RT "LC3 conjugation system in mammalian autophagy.";
RL Int. J. Biochem. Cell Biol. 36:2503-2518(2004).
RN [8]
RP INTERACTION WITH CABP1.
RX PubMed=15095872; DOI=10.1016/j.jmb.2003.12.054;
RA Seidenbecher C.I., Landwehr M., Smalla K.H., Kreutz M., Dieterich D.C.,
RA Zuschratter W., Reissner C., Hammarback J.A., Bockers T.M.,
RA Gundelfinger E.D., Kreutz M.R.;
RT "Caldendrin but not calmodulin binds to light chain 3 of MAP1A/B: an
RT association with the microtubule cytoskeleton highlighting exclusive
RT binding partners for neuronal Ca(2+)-sensor proteins.";
RL J. Mol. Biol. 336:957-970(2004).
RN [9]
RP CLEAVAGE BY ATG4B, AND MUTAGENESIS OF GLN-116; PHE-119 AND GLY-120.
RX PubMed=16183633; DOI=10.1074/jbc.m509158200;
RA Sugawara K., Suzuki N.N., Fujioka Y., Mizushima N., Ohsumi Y., Inagaki F.;
RT "Structural basis for the specificity and catalysis of human Atg4B
RT responsible for mammalian autophagy.";
RL J. Biol. Chem. 280:40058-40065(2005).
RN [10]
RP CLEAVAGE BY ATG4B.
RX PubMed=16874114; DOI=10.4161/auto.2744;
RA Yoshimura K., Shibata M., Koike M., Gotoh K., Fukaya M., Watanabe M.,
RA Uchiyama Y.;
RT "Effects of RNA interference of Atg4B on the limited proteolysis of LC3 in
RT PC12 cells and expression of Atg4B in various rat tissues.";
RL Autophagy 2:200-208(2006).
RN [11]
RP INTERACTION WITH PLCL1.
RX PubMed=23399561; DOI=10.1016/j.bbrc.2013.01.119;
RA Umebayashi H., Mizokami A., Matsuda M., Harada K., Takeuchi H., Tanida I.,
RA Hirata M., Kanematsu T.;
RT "Phospholipase C-related catalytically inactive protein, a novel
RT microtubule-associated protein 1 light chain 3-binding protein, negatively
RT regulates autophagosome formation.";
RL Biochem. Biophys. Res. Commun. 432:268-274(2013).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF 1-120.
RX PubMed=15265004; DOI=10.1111/j.1356-9597.2004.00750.x;
RA Sugawara K., Suzuki N.N., Fujioka Y., Mizushima N., Ohsumi Y., Inagaki F.;
RT "The crystal structure of microtubule-associated protein light chain 3, a
RT mammalian homologue of Saccharomyces cerevisiae Atg8.";
RL Genes Cells 9:611-618(2004).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-124 IN COMPLEX WITH ATG4B.
RX PubMed=19322194; DOI=10.1038/emboj.2009.80;
RA Satoo K., Noda N.N., Kumeta H., Fujioka Y., Mizushima N., Ohsumi Y.,
RA Inagaki F.;
RT "The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing
RT and delipidation during autophagy.";
RL EMBO J. 28:1341-1350(2009).
CC -!- FUNCTION: Ubiquitin-like modifier involved in formation of
CC autophagosomal vacuoles (autophagosomes). Plays a role in mitophagy
CC which contributes to regulate mitochondrial quantity and quality by
CC eliminating the mitochondria to a basal level to fulfill cellular
CC energy requirements and preventing excess ROS production. In response
CC to cellular stress and upon mitochondria fission, binds C-18 ceramides
CC and anchors autophagolysosomes to outer mitochondrial membranes to
CC eliminate damaged mitochondria. While LC3s are involved in elongation
CC of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential
CC for a later stage in autophagosome maturation. Promotes primary
CC ciliogenesis by removing OFD1 from centriolar satellites via the
CC autophagic pathway. Through its interaction with the reticulophagy
CC receptor TEX264, participates in the remodeling of subdomains of the
CC endoplasmic reticulum into autophagosomes upon nutrient stress, which
CC then fuse with lysosomes for endoplasmic reticulum turnover. Upon
CC nutrient stress, directly recruits cofactor JMY to the phagophore
CC membrane surfaces and promotes JMY's actin nucleation activity and
CC autophagosome biogenesis during autophagy.
CC {ECO:0000250|UniProtKB:Q9GZQ8}.
CC -!- SUBUNIT: 3 different light chains, LC1, LC2 and LC3, can associate with
CC MAP1A and MAP1B proteins (PubMed:7908909). Interacts at microtubules
CC with CABP1 (via EF-hands 1 and 2) but not with calmodulin
CC (PubMed:15095872). Interacts with FYCO1 (via C-terminus). Interacts
CC with TP53INP1 and TP53INP2. Interacts with TBC1D25. Directly interacts
CC with SQSTM1; this interaction leads to MAP1LC3B recruitment to
CC inclusion bodies containing polyubiquitinated protein aggregates and to
CC inclusion body degradation by autophagy (By similarity). Interacts with
CC ATG4B (PubMed:19322194). Interacts with MAPK15 and BNIP3. Interacts
CC with MAPB1, KEAP1, PCM1, OFD1, CEP131, and TECPR2. Interacts with
CC TBC1D5. Found in a complex with UBQLN1 and UBQLN2. Interacts with
CC UBQLN4 (via STI1 1 and 2 domains). Interacts with UBQLN1 in the
CC presence of UBQLN4. Interacts with ATG13. Interacts with RETREG1,
CC RETREG2 and RETREG3 (By similarity). Interacts with PLCL1; the
CC interaction inhibits autophagosome formation (PubMed:23399561).
CC Interacts with TRIM16 (By similarity). Interacts with CRY1 and PER2 (By
CC similarity). Interacts with the reticulophagy receptor TEX264 (By
CC similarity). Membrane-bound form LC3-II interacts with PHB1 and PHB2;
CC the interaction takes place upon Parkin-mediated mitochondrial damage
CC (By similarity). Interacts with PJVK; the interaction is direct (By
CC similarity). Interacts with KBTBD6 and KBTBD7; the interaction is
CC direct (By similarity). Interacts with AMBRA1 (via LIR motif) (By
CC similarity). Interacts with JMY; the interaction results in the
CC activation of JYM's nucleation activity in the cytoplasm (By
CC similarity). Interacts with MOAP1 (via LIR motif) (By similarity).
CC {ECO:0000250|UniProtKB:Q9CQV6, ECO:0000250|UniProtKB:Q9GZQ8,
CC ECO:0000269|PubMed:15095872, ECO:0000269|PubMed:19322194,
CC ECO:0000269|PubMed:23399561, ECO:0000269|PubMed:7908909}.
CC -!- SUBCELLULAR LOCATION: Cytoplasmic vesicle, autophagosome membrane
CC {ECO:0000269|PubMed:11060023}; Lipid-anchor
CC {ECO:0000269|PubMed:11060023}. Endomembrane system
CC {ECO:0000269|PubMed:11060023}; Lipid-anchor
CC {ECO:0000269|PubMed:11060023}. Mitochondrion membrane
CC {ECO:0000250|UniProtKB:Q9GZQ8}; Lipid-anchor
CC {ECO:0000250|UniProtKB:Q9GZQ8}. Cytoplasm, cytoskeleton
CC {ECO:0000269|PubMed:11060023}. Cytoplasmic vesicle
CC {ECO:0000250|UniProtKB:Q9GZQ8}. Note=LC3-II binds to the autophagic
CC membranes. LC3-II localizes with the mitochondrial inner membrane
CC during Parkin-mediated mitophagy (By similarity). Localizes also to
CC discrete punctae along the ciliary axoneme (By similarity).
CC {ECO:0000250|UniProtKB:Q9GZQ8}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q62625-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q62625-2; Sequence=VSP_012092;
CC -!- TISSUE SPECIFICITY: Abundant only in neurons. Detected in testes.
CC {ECO:0000269|PubMed:7908909}.
CC -!- PTM: The precursor molecule is cleaved by ATG4 (ATG4A, ATG4B, ATG4C or
CC ATG4D) to expose the glycine at the C-terminus and form the cytosolic
CC form, LC3-I (PubMed:11060023, PubMed:16183633, PubMed:16874114). The
CC processed form is then activated by APG7L/ATG7, transferred to ATG3 and
CC conjugated to phosphatidylethanolamine (PE) phospholipid to form the
CC membrane-bound form, LC3-II. During non-canonical autophagy, the
CC processed form is conjugated to phosphatidylserine (PS) phospholipid.
CC ATG4 proteins also mediate the delipidation of PE-conjugated forms. In
CC addition, ATG4B and ATG4D mediate delipidation of ATG8 proteins
CC conjugated to PS during non-canonical autophagy. ATG4B constitutes the
CC major protein for proteolytic activation (By similarity). ATG4D is the
CC main enzyme for delipidation activity (By similarity).
CC {ECO:0000250|UniProtKB:Q9CQV6, ECO:0000250|UniProtKB:Q9GZQ8,
CC ECO:0000269|PubMed:11060023, ECO:0000269|PubMed:16183633,
CC ECO:0000269|PubMed:16874114}.
CC -!- PTM: Phosphorylation by PKA inhibits conjugation of
CC phosphatidylethanolamine (PE). Interaction with MAPK15 reduces the
CC inhibitory phosphorylation and increases autophagy activity.
CC {ECO:0000250|UniProtKB:Q9GZQ8}.
CC -!- SIMILARITY: Belongs to the ATG8 family. {ECO:0000305}.
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DR EMBL; U05784; AAA20645.1; -; mRNA.
DR EMBL; AY206669; AAP42561.1; -; mRNA.
DR EMBL; AY392036; AAQ94605.1; -; mRNA.
DR EMBL; BC058144; AAH58144.1; -; mRNA.
DR EMBL; BC083556; AAH83556.1; -; mRNA.
DR PIR; A53624; A53624.
DR RefSeq; NP_074058.2; NM_022867.2. [Q62625-2]
DR RefSeq; XP_017456840.1; XM_017601351.1. [Q62625-1]
DR PDB; 1UGM; X-ray; 2.05 A; A=1-120.
DR PDB; 2K6Q; NMR; -; A=1-120.
DR PDB; 2Z0D; X-ray; 1.90 A; B=1-120.
DR PDB; 2Z0E; X-ray; 1.90 A; B=1-124.
DR PDB; 2ZZP; X-ray; 2.05 A; B=1-124.
DR PDBsum; 1UGM; -.
DR PDBsum; 2K6Q; -.
DR PDBsum; 2Z0D; -.
DR PDBsum; 2Z0E; -.
DR PDBsum; 2ZZP; -.
DR AlphaFoldDB; Q62625; -.
DR BMRB; Q62625; -.
DR SMR; Q62625; -.
DR BioGRID; 249213; 5.
DR ELM; Q62625; -.
DR IntAct; Q62625; 7.
DR MINT; Q62625; -.
DR PhosphoSitePlus; Q62625; -.
DR jPOST; Q62625; -.
DR PRIDE; Q62625; -.
DR GeneID; 64862; -.
DR KEGG; rno:64862; -.
DR UCSC; RGD:621315; rat. [Q62625-1]
DR CTD; 81631; -.
DR RGD; 621315; Map1lc3b.
DR VEuPathDB; HostDB:ENSRNOG00000017905; -.
DR eggNOG; KOG1654; Eukaryota.
DR HOGENOM; CLU_119276_1_0_1; -.
DR InParanoid; Q62625; -.
DR OMA; EFSHDER; -.
DR OrthoDB; 1508198at2759; -.
DR Reactome; R-RNO-1632852; Macroautophagy.
DR Reactome; R-RNO-5205685; PINK1-PRKN Mediated Mitophagy.
DR Reactome; R-RNO-8854214; TBC/RABGAPs.
DR Reactome; R-RNO-8934903; Receptor Mediated Mitophagy.
DR Reactome; R-RNO-9664873; Pexophagy.
DR Reactome; R-RNO-9755511; KEAP1-NFE2L2 pathway.
DR EvolutionaryTrace; Q62625; -.
DR PRO; PR:Q62625; -.
DR Proteomes; UP000002494; Chromosome 19.
DR Bgee; ENSRNOG00000017905; Expressed in cerebellum and 20 other tissues.
DR ExpressionAtlas; Q62625; baseline and differential.
DR Genevisible; Q62625; RN.
DR GO; GO:0044754; C:autolysosome; ISO:RGD.
DR GO; GO:0005776; C:autophagosome; ISO:RGD.
DR GO; GO:0000421; C:autophagosome membrane; IDA:UniProtKB.
DR GO; GO:0030424; C:axon; IDA:RGD.
DR GO; GO:0005930; C:axoneme; ISO:RGD.
DR GO; GO:0005737; C:cytoplasm; IDA:RGD.
DR GO; GO:0031410; C:cytoplasmic vesicle; ISS:UniProtKB.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0030425; C:dendrite; IDA:RGD.
DR GO; GO:0012505; C:endomembrane system; IEA:UniProtKB-SubCell.
DR GO; GO:0016020; C:membrane; ISO:RGD.
DR GO; GO:0005874; C:microtubule; IEA:UniProtKB-KW.
DR GO; GO:0005875; C:microtubule associated complex; IDA:RGD.
DR GO; GO:0031966; C:mitochondrial membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005739; C:mitochondrion; ISO:RGD.
DR GO; GO:0043025; C:neuronal cell body; IDA:RGD.
DR GO; GO:0097001; F:ceramide binding; ISO:RGD.
DR GO; GO:0008017; F:microtubule binding; IDA:RGD.
DR GO; GO:0019904; F:protein domain specific binding; IPI:RGD.
DR GO; GO:0015631; F:tubulin binding; IDA:RGD.
DR GO; GO:0031625; F:ubiquitin protein ligase binding; ISO:RGD.
DR GO; GO:0000045; P:autophagosome assembly; IBA:GO_Central.
DR GO; GO:0097352; P:autophagosome maturation; ISO:RGD.
DR GO; GO:0006914; P:autophagy; ISO:RGD.
DR GO; GO:0000422; P:autophagy of mitochondrion; ISO:RGD.
DR GO; GO:0006995; P:cellular response to nitrogen starvation; IBA:GO_Central.
DR GO; GO:0009267; P:cellular response to starvation; ISS:UniProtKB.
DR GO; GO:0016236; P:macroautophagy; ISO:RGD.
DR GO; GO:0000423; P:mitophagy; ISS:UniProtKB.
DR GO; GO:0070257; P:positive regulation of mucus secretion; ISO:RGD.
DR GO; GO:0032092; P:positive regulation of protein binding; IDA:RGD.
DR IDEAL; IID50112; -.
DR InterPro; IPR004241; Atg8-like.
DR InterPro; IPR029071; Ubiquitin-like_domsf.
DR PANTHER; PTHR10969; PTHR10969; 1.
DR Pfam; PF02991; ATG8; 1.
DR SUPFAM; SSF54236; SSF54236; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Autophagy; Cytoplasm;
KW Cytoplasmic vesicle; Cytoskeleton; Direct protein sequencing; Lipoprotein;
KW Membrane; Microtubule; Mitochondrion; Phosphoprotein; Reference proteome;
KW Ubl conjugation pathway.
FT CHAIN 1..120
FT /note="Microtubule-associated proteins 1A/1B light chain
FT 3B"
FT /id="PRO_0000017202"
FT PROPEP 121..142
FT /note="Removed in mature form"
FT /id="PRO_0000017203"
FT SITE 120..121
FT /note="Cleavage; by ATG4B"
FT /evidence="ECO:0000269|PubMed:11060023,
FT ECO:0000269|PubMed:16183633"
FT LIPID 120
FT /note="Phosphatidylethanolamine amidated glycine;
FT alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9GZQ8"
FT LIPID 120
FT /note="Phosphatidylserine amidated glycine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9GZQ8"
FT VAR_SEQ 126..142
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334, ECO:0000303|Ref.2,
FT ECO:0000303|Ref.3"
FT /id="VSP_012092"
FT MUTAGEN 116
FT /note="Q->A: No processing of precursor."
FT /evidence="ECO:0000269|PubMed:16183633"
FT MUTAGEN 119
FT /note="F->A: No processing of precursor."
FT /evidence="ECO:0000269|PubMed:16183633"
FT MUTAGEN 120
FT /note="G->A: No processing of precursor."
FT /evidence="ECO:0000269|PubMed:11060023,
FT ECO:0000269|PubMed:16183633"
FT HELIX 7..10
FT /evidence="ECO:0007829|PDB:2Z0D"
FT HELIX 13..26
FT /evidence="ECO:0007829|PDB:2Z0D"
FT STRAND 30..37
FT /evidence="ECO:0007829|PDB:2Z0D"
FT STRAND 51..55
FT /evidence="ECO:0007829|PDB:2Z0D"
FT HELIX 60..70
FT /evidence="ECO:0007829|PDB:2Z0D"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:2K6Q"
FT STRAND 80..83
FT /evidence="ECO:0007829|PDB:2Z0D"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:1UGM"
FT HELIX 95..102
FT /evidence="ECO:0007829|PDB:2Z0D"
FT STRAND 109..114
FT /evidence="ECO:0007829|PDB:2Z0D"
SQ SEQUENCE 142 AA; 16394 MW; D07E9D063C125E32 CRC64;
MPSEKTFKQR RSFEQRVEDV RLIREQHPTK IPVIIERYKG EKQLPVLDKT KFLVPDHVNM
SELIKIIRRR LQLNANQAFF LLVNGHSMVS VSTPISEVYE SERDEDGFLY MVYASQETFG
TALAVTYMSA LKATATGREP CL
