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Q62625 (MLP3B_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 112. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:Map1lc3b
Synonyms:Map1alc3, Map1lc3
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length142 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

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, AZI1, and TECPR2 By similarity. Interacts with ATG4B. Ref.8

Subcellular location

Cytoplasmcytoskeleton. Endomembrane system; Lipid-anchor. Cytoplasmic vesicleautophagosome membrane; Lipid-anchor. Note: LC3-II binds to the autophagic membranes. Localizes also to discrete punctae along the ciliary axoneme By similarity. Ref.6

Tissue specificity

Abundant only in neurons. Detected in testes.

Post-translational modification

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. Ref.6 Ref.9 Ref.10

Phosphorylation at Ser-12 by PKA inhibits conjugation to phosphatidylethanolamine (PE) By similarity. Interaction with MAPK15 reduces the inhibitory phosphorylation and increases autophagy activity By similarity.

Sequence similarities

Belongs to the ATG8 family.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q62625-1)

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.
Isoform 2 (identifier: Q62625-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 120119Microtubule-associated proteins 1A/1B light chain 3B
PRO_0000017202
Propeptide121 – 14222Removed in mature form
PRO_0000017203

Sites

Site120 – 1212Cleavage; by ATG4B

Amino acid modifications

Modified residue121Phosphoserine; by PKA By similarity
Lipidation1201Phosphatidylethanolamine amidated glycine By similarity

Natural variations

Alternative sequence126 – 14217Missing in isoform 2.
VSP_012092

Experimental info

Mutagenesis1161Q → A: No processing of precursor. Ref.9
Mutagenesis1191F → A: No processing of precursor. Ref.9
Mutagenesis1201G → A: No processing of precursor. Ref.6 Ref.9

Secondary structure

.................... 142
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: D07E9D063C125E32

FASTA14216,394
        10         20         30         40         50         60 
MPSEKTFKQR RSFEQRVEDV RLIREQHPTK IPVIIERYKG EKQLPVLDKT KFLVPDHVNM 

        70         80         90        100        110        120 
SELIKIIRRR LQLNANQAFF LLVNGHSMVS VSTPISEVYE SERDEDGFLY MVYASQETFG 

       130        140 
TALAVTYMSA LKATATGREP CL 

« Hide

Isoform 2 [UniParc].

Checksum: 520E28B28163FA8D
Show »

FASTA12514,599

References

« Hide 'large scale' references
[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]"LC3 conjugation system in mammalian autophagy."
Tanida I., Ueno T., Kominami E.
Int. J. Biochem. Cell Biol. 36:2503-2518(2004) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRA53624.
RefSeqNP_074058.2. NM_022867.2.
UniGeneRn.41412.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1UGMX-ray2.05A1-120[»]
2K6QNMR-A1-120[»]
2Z0DX-ray1.90B1-120[»]
2Z0EX-ray1.90B1-124[»]
2ZZPX-ray2.05B1-124[»]
ProteinModelPortalQ62625.
SMRQ62625. Positions 5-122.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid249213. 2 interactions.
IntActQ62625. 6 interactions.

PTM databases

PhosphoSiteQ62625.

Proteomic databases

PaxDbQ62625.
PRIDEQ62625.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000067141; ENSRNOP00000062130; ENSRNOG00000017905. [Q62625-2]
GeneID64862.
KEGGrno:64862.
UCSCRGD:621315. rat. [Q62625-1]

Organism-specific databases

CTD81631.
RGD621315. Map1lc3b.

Phylogenomic databases

eggNOGNOG283348.
GeneTreeENSGT00390000012937.
HOGENOMHOG000232034.
HOVERGENHBG051706.
InParanoidQ62625.
KOK10435.
OMAIRDQHPT.

Gene expression databases

ArrayExpressQ62625.
GenevestigatorQ62625.

Family and domain databases

InterProIPR004241. Atg8_like.
[Graphical view]
PANTHERPTHR10969. PTHR10969. 1 hit.
PfamPF02991. Atg8. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ62625.
NextBio613772.
PROQ62625.

Entry information

Entry nameMLP3B_RAT
AccessionPrimary (citable) accession number: Q62625
Secondary accession number(s): Q6XVN7
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 112 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references