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Q62625

- MLP3B_RAT

UniProt

Q62625 - MLP3B_RAT

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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

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
Complete GO annotation...

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. microtubule Source: UniProtKB-KW
  7. microtubule associated complex Source: RGD
  8. neuronal cell body Source: RGD
Complete GO annotation...

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

ExpressionAtlasiQ62625. baseline and differential.
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. 3 interactions.
IntActiQ62625. 7 interactions.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MPSEKTFKQR RSFEQRVEDV RLIREQHPTK IPVIIERYKG EKQLPVLDKT
60 70 80 90 100
KFLVPDHVNM SELIKIIRRR LQLNANQAFF LLVNGHSMVS VSTPISEVYE
110 120 130 140
SERDEDGFLY MVYASQETFG TALAVTYMSA LKATATGREP CL
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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. 3 interactions.
IntActi Q62625. 7 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

ExpressionAtlasi Q62625. baseline and differential.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 118 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