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Q62625

- MLP3B_RAT

UniProt

Q62625 - MLP3B_RAT

Protein

Microtubule-associated proteins 1A/1B light chain 3B

Gene

Map1lc3b

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 116 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Ubiquitin-like modifier involved in formation of autophagosomal vacuoles (autophagosomes). Plays a role in mitophagy which contributes to regulate mitochondrial quantity and quality by eliminating the mitochondria to a basal level to fulfill cellular energy requirements and preventing excess ROS production. Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei120 – 1212Cleavage; by ATG4B

    GO - Molecular functioni

    1. microtubule binding Source: RGD
    2. protein domain specific binding Source: RGD
    3. tubulin binding Source: RGD

    GO - Biological processi

    1. autophagy Source: UniProtKB-KW
    2. positive regulation of protein binding Source: RGD

    Keywords - Biological processi

    Autophagy, Ubl conjugation pathway

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Microtubule-associated proteins 1A/1B light chain 3B
    Alternative name(s):
    Autophagy-related protein LC3 B
    Autophagy-related ubiquitin-like modifier LC3 B
    MAP1 light chain 3-like protein 2
    MAP1A/MAP1B light chain 3 B
    Short name:
    MAP1A/MAP1B LC3 B
    Microtubule-associated protein 1 light chain 3 beta
    Gene namesi
    Name:Map1lc3b
    Synonyms:Map1alc3, Map1lc3
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Chromosome 19

    Organism-specific databases

    RGDi621315. Map1lc3b.

    Subcellular locationi

    Cytoplasmcytoskeleton 1 Publication. Endomembrane system 1 Publication; Lipid-anchor 1 Publication. Cytoplasmic vesicleautophagosome membrane 1 Publication; Lipid-anchor 1 Publication
    Note: LC3-II binds to the autophagic membranes. Localizes also to discrete punctae along the ciliary axoneme By similarity.By similarity

    GO - Cellular componenti

    1. autophagic vacuole membrane Source: UniProtKB
    2. axon Source: RGD
    3. cytoplasm Source: RGD
    4. cytoplasmic vesicle Source: UniProtKB-KW
    5. dendrite Source: RGD
    6. endomembrane system Source: UniProtKB-SubCell
    7. microtubule Source: UniProtKB-KW
    8. microtubule associated complex Source: RGD
    9. neuronal cell body Source: RGD

    Keywords - Cellular componenti

    Cytoplasm, Cytoplasmic vesicle, Cytoskeleton, Membrane, Microtubule

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi116 – 1161Q → A: No processing of precursor. 1 Publication
    Mutagenesisi119 – 1191F → A: No processing of precursor. 1 Publication
    Mutagenesisi120 – 1201G → A: No processing of precursor. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 120119Microtubule-associated proteins 1A/1B light chain 3BPRO_0000017202Add
    BLAST
    Propeptidei121 – 14222Removed in mature formPRO_0000017203Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei12 – 121Phosphoserine; by PKABy similarity
    Lipidationi120 – 1201Phosphatidylethanolamine amidated glycineBy similarity

    Post-translational modificationi

    The precursor molecule is cleaved by APG4B/ATG4B to form LC3-I. This is activated by APG7L/ATG7, transferred to ATG3 and conjugated to phospholipid to form LC3-II.3 Publications
    Phosphorylation at Ser-12 by PKA inhibits conjugation to phosphatidylethanolamine (PE). Interaction with MAPK15 reduces the inhibitory phosphorylation and increases autophagy activity.By similarity

    Keywords - PTMi

    Lipoprotein, Phosphoprotein

    Proteomic databases

    PaxDbiQ62625.
    PRIDEiQ62625.

    PTM databases

    PhosphoSiteiQ62625.

    Expressioni

    Tissue specificityi

    Abundant only in neurons. Detected in testes.

    Gene expression databases

    ArrayExpressiQ62625.
    GenevestigatoriQ62625.

    Interactioni

    Subunit structurei

    3 different light chains, LC1, LC2 and LC3, can associate with MAP1A and MAP1B proteins. Interacts at microtubules with CABP1 (via EF-hands 1 and 2) but not with calmodulin. A calcium-dependent binding site is located at the C-terminus while a calcium-independent binding site is located at the N-terminus. Interacts with FYCO1 (via C-terminus) By similarity. Interacts with TP53INP1 and TP53INP2 By similarity. Interacts with TBC1D25 By similarity. Directly interacts with SQSTM1; this interaction leads to MAP1LC3B recruitment to inclusion bodies containing polyubiquitinated protein aggregates and to inclusion body degradation by autophagy By similarity. Interacts with MAPK15 and BNIP3 By similarity. Interacts with MAPB1, KEAP1, PCM1, OFD1, CEP131, and TECPR2 By similarity. Interacts with ATG4B.By similarity2 Publications

    Protein-protein interaction databases

    BioGridi249213. 2 interactions.
    IntActiQ62625. 6 interactions.

    Structurei

    Secondary structure

    1
    142
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi7 – 104
    Helixi13 – 2614
    Beta strandi30 – 378
    Beta strandi51 – 555
    Helixi60 – 7011
    Beta strandi75 – 773
    Beta strandi80 – 834
    Beta strandi91 – 944
    Helixi95 – 1028
    Beta strandi109 – 1146

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1UGMX-ray2.05A1-120[»]
    2K6QNMR-A1-120[»]
    2Z0DX-ray1.90B1-120[»]
    2Z0EX-ray1.90B1-124[»]
    2ZZPX-ray2.05B1-124[»]
    ProteinModelPortaliQ62625.
    SMRiQ62625. Positions 5-122.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ62625.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ATG8 family.Curated

    Phylogenomic databases

    eggNOGiNOG283348.
    GeneTreeiENSGT00390000012937.
    HOGENOMiHOG000232034.
    HOVERGENiHBG051706.
    InParanoidiQ62625.
    KOiK10435.
    OMAiIRDQHPT.

    Family and domain databases

    InterProiIPR004241. Atg8_like.
    IPR029071. Ubiquitin-rel_dom.
    [Graphical view]
    PANTHERiPTHR10969. PTHR10969. 1 hit.
    PfamiPF02991. Atg8. 1 hit.
    [Graphical view]
    SUPFAMiSSF54236. SSF54236. 1 hit.

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q62625-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MPSEKTFKQR RSFEQRVEDV RLIREQHPTK IPVIIERYKG EKQLPVLDKT    50
    KFLVPDHVNM SELIKIIRRR LQLNANQAFF LLVNGHSMVS VSTPISEVYE 100
    SERDEDGFLY MVYASQETFG TALAVTYMSA LKATATGREP CL 142
    Length:142
    Mass (Da):16,394
    Last modified:January 23, 2007 - v3
    Checksum:iD07E9D063C125E32
    GO
    Isoform 2 (identifier: Q62625-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         126-142: Missing.

    Show »
    Length:125
    Mass (Da):14,599
    Checksum:i520E28B28163FA8D
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei126 – 14217Missing in isoform 2. 3 PublicationsVSP_012092Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U05784 mRNA. Translation: AAA20645.1.
    AY206669 mRNA. Translation: AAP42561.1.
    AY392036 mRNA. Translation: AAQ94605.1.
    BC058144 mRNA. Translation: AAH58144.1.
    BC083556 mRNA. Translation: AAH83556.1.
    PIRiA53624.
    RefSeqiNP_074058.2. NM_022867.2. [Q62625-2]
    UniGeneiRn.41412.

    Genome annotation databases

    EnsembliENSRNOT00000067141; ENSRNOP00000062130; ENSRNOG00000017905. [Q62625-2]
    GeneIDi64862.
    KEGGirno:64862.
    UCSCiRGD:621315. rat. [Q62625-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U05784 mRNA. Translation: AAA20645.1 .
    AY206669 mRNA. Translation: AAP42561.1 .
    AY392036 mRNA. Translation: AAQ94605.1 .
    BC058144 mRNA. Translation: AAH58144.1 .
    BC083556 mRNA. Translation: AAH83556.1 .
    PIRi A53624.
    RefSeqi NP_074058.2. NM_022867.2. [Q62625-2 ]
    UniGenei Rn.41412.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1UGM X-ray 2.05 A 1-120 [» ]
    2K6Q NMR - A 1-120 [» ]
    2Z0D X-ray 1.90 B 1-120 [» ]
    2Z0E X-ray 1.90 B 1-124 [» ]
    2ZZP X-ray 2.05 B 1-124 [» ]
    ProteinModelPortali Q62625.
    SMRi Q62625. Positions 5-122.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 249213. 2 interactions.
    IntActi Q62625. 6 interactions.

    PTM databases

    PhosphoSitei Q62625.

    Proteomic databases

    PaxDbi Q62625.
    PRIDEi Q62625.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000067141 ; ENSRNOP00000062130 ; ENSRNOG00000017905 . [Q62625-2 ]
    GeneIDi 64862.
    KEGGi rno:64862.
    UCSCi RGD:621315. rat. [Q62625-1 ]

    Organism-specific databases

    CTDi 81631.
    RGDi 621315. Map1lc3b.

    Phylogenomic databases

    eggNOGi NOG283348.
    GeneTreei ENSGT00390000012937.
    HOGENOMi HOG000232034.
    HOVERGENi HBG051706.
    InParanoidi Q62625.
    KOi K10435.
    OMAi IRDQHPT.

    Miscellaneous databases

    EvolutionaryTracei Q62625.
    NextBioi 613772.
    PROi Q62625.

    Gene expression databases

    ArrayExpressi Q62625.
    Genevestigatori Q62625.

    Family and domain databases

    InterProi IPR004241. Atg8_like.
    IPR029071. Ubiquitin-rel_dom.
    [Graphical view ]
    PANTHERi PTHR10969. PTHR10969. 1 hit.
    Pfami PF02991. Atg8. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54236. SSF54236. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Molecular characterization of light chain 3. A microtubule binding subunit of MAP1A and MAP1B."
      Mann S.S., Hammarback J.A.
      J. Biol. Chem. 269:11492-11497(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Tissue: Brain.
    2. "Cloning and characterization of rat lc3 orthologs."
      Dang Y., Yu L., Wu J., Pei Y.
      Submitted (DEC-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
      Strain: Sprague-Dawley.
      Tissue: Brain.
    3. "Rattus norvegicus microtubule-associated protein 1 light chain 3 (Map1lc3)."
      Zhou G., Dai F., Yu L.
      Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
      Strain: Sprague-Dawley.
    4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Tissue: Heart and Pituitary.
    5. Lubec G., Kang S.U.
      Submitted (JUL-2007) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 31-37, IDENTIFICATION BY MASS SPECTROMETRY.
      Strain: Sprague-Dawley.
      Tissue: Brain.
    6. "LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing."
      Kabeya Y., Mizushima N., Ueno T., Yamamoto A., Kirisako T., Noda T., Kominami E., Ohsumi Y., Yoshimori T.
      EMBO J. 19:5720-5728(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, CLEAVAGE, MUTAGENESIS OF GLY-120.
    7. Cited for: REVIEW.
    8. "Caldendrin but not calmodulin binds to light chain 3 of MAP1A/B: an association with the microtubule cytoskeleton highlighting exclusive binding partners for neuronal Ca(2+)-sensor proteins."
      Seidenbecher C.I., Landwehr M., Smalla K.H., Kreutz M., Dieterich D.C., Zuschratter W., Reissner C., Hammarback J.A., Bockers T.M., Gundelfinger E.D., Kreutz M.R.
      J. Mol. Biol. 336:957-970(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH CABP1.
    9. "Structural basis for the specificity and catalysis of human Atg4B responsible for mammalian autophagy."
      Sugawara K., Suzuki N.N., Fujioka Y., Mizushima N., Ohsumi Y., Inagaki F.
      J. Biol. Chem. 280:40058-40065(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: CLEAVAGE BY ATG4B, MUTAGENESIS OF GLN-116; PHE-119 AND GLY-120.
    10. "Effects of RNA interference of Atg4B on the limited proteolysis of LC3 in PC12 cells and expression of Atg4B in various rat tissues."
      Yoshimura K., Shibata M., Koike M., Gotoh K., Fukaya M., Watanabe M., Uchiyama Y.
      Autophagy 2:200-208(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: CLEAVAGE BY ATG4B.
    11. "The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8."
      Sugawara K., Suzuki N.N., Fujioka Y., Mizushima N., Ohsumi Y., Inagaki F.
      Genes Cells 9:611-618(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF 1-120.
    12. "The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy."
      Satoo K., Noda N.N., Kumeta H., Fujioka Y., Mizushima N., Ohsumi Y., Inagaki F.
      EMBO J. 28:1341-1350(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-124 IN COMPLEX WITH ATG4B.

    Entry informationi

    Entry nameiMLP3B_RAT
    AccessioniPrimary (citable) accession number: Q62625
    Secondary accession number(s): Q6XVN7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 116 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3