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Protein

Ubiquitin-like protein ATG12B

Gene

ATG12B

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Ubiquitin-like protein involved in cytoplasm to vacuole transport (Cvt) and autophagy vesicles formation. Conjugation with ATG5 through a ubiquitin-like conjugating system involving also ATG7 as an E1-like activating enzyme and ATG10 as an E2-like conjugating enzyme, is essential for its function. ATG12/ATG5 conjugate has an essential role in plant nutrient recycling.1 Publication

GO - Molecular functioni

GO - Biological processi

  • autophagosome assembly Source: GO_Central
  • autophagy Source: TAIR
  • C-terminal protein lipidation Source: GO_Central
  • mitophagy Source: GO_Central
  • nucleophagy Source: GO_Central
  • protein transport Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Autophagy, Protein transport, Transport, Ubl conjugation pathway

Enzyme and pathway databases

ReactomeiR-ATH-1632852. Macroautophagy.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-like protein ATG12B
Alternative name(s):
Autophagy-related protein 12b
Short name:
APG12-like protein b
Short name:
AtAPG12b
Gene namesi
Name:ATG12B
Synonyms:APG12, APG12B
Ordered Locus Names:At3g13970
ORF Names:MDC16.9
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G13970.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 9493Ubiquitin-like protein ATG12BPRO_0000250543Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Cross-linki94 – 94Glycyl lysine isopeptide (Gly-Lys) (interchain with K-128 in ATG5)By similarity

Keywords - PTMi

Acetylation, Isopeptide bond

Proteomic databases

PaxDbiQ9LVK3.

Expressioni

Tissue specificityi

Ubiquitous.1 Publication

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
ATG3Q0WWQ12EBI-8276588,EBI-8276607

Protein-protein interaction databases

BioGridi5945. 1 interaction.
IntActiQ9LVK3. 1 interaction.
STRINGi3702.AT3G13970.1.

Structurei

Secondary structure

1
94
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi11 – 188Combined sources
Beta strandi29 – 335Combined sources
Helixi39 – 4911Combined sources
Beta strandi55 – 628Combined sources
Helixi70 – 778Combined sources
Beta strandi82 – 898Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WZ3X-ray1.80A/B1-94[»]
ProteinModelPortaliQ9LVK3.
SMRiQ9LVK3. Positions 10-93.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9LVK3.

Family & Domainsi

Sequence similaritiesi

Belongs to the ATG12 family.Curated

Phylogenomic databases

eggNOGiKOG3439. Eukaryota.
ENOG4111ND7. LUCA.
HOGENOMiHOG000234863.
InParanoidiQ9LVK3.
KOiK08336.
OMAiIGRISEF.
PhylomeDBiQ9LVK3.

Family and domain databases

InterProiIPR007242. Atg12.
IPR029071. Ubiquitin-rel_dom.
[Graphical view]
PANTHERiPTHR13385. PTHR13385. 1 hit.
PfamiPF04110. APG12. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q9LVK3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATESPNSVQ KIVVHLRATG GAPILKQSKF KVSGSDKFAN VIDFLRRQLH
60 70 80 90
SDSLFVYVNS AFSPNPDESV IDLYNNFGFD GKLVVNYACS MAWG
Length:94
Mass (Da):10,358
Last modified:October 1, 2000 - v1
Checksum:i5BA77795F9C89D6A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB073185 mRNA. Translation: BAB88397.1.
AB019229 Genomic DNA. Translation: BAB02327.1.
CP002686 Genomic DNA. Translation: AEE75446.1.
BT024653 mRNA. Translation: ABD57478.1.
AK118997 mRNA. Translation: BAC43573.1.
RefSeqiNP_188013.2. NM_112251.3.
UniGeneiAt.39312.

Genome annotation databases

EnsemblPlantsiAT3G13970.1; AT3G13970.1; AT3G13970.
GeneIDi820611.
GrameneiAT3G13970.1; AT3G13970.1; AT3G13970.
KEGGiath:AT3G13970.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB073185 mRNA. Translation: BAB88397.1.
AB019229 Genomic DNA. Translation: BAB02327.1.
CP002686 Genomic DNA. Translation: AEE75446.1.
BT024653 mRNA. Translation: ABD57478.1.
AK118997 mRNA. Translation: BAC43573.1.
RefSeqiNP_188013.2. NM_112251.3.
UniGeneiAt.39312.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WZ3X-ray1.80A/B1-94[»]
ProteinModelPortaliQ9LVK3.
SMRiQ9LVK3. Positions 10-93.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi5945. 1 interaction.
IntActiQ9LVK3. 1 interaction.
STRINGi3702.AT3G13970.1.

Proteomic databases

PaxDbiQ9LVK3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G13970.1; AT3G13970.1; AT3G13970.
GeneIDi820611.
GrameneiAT3G13970.1; AT3G13970.1; AT3G13970.
KEGGiath:AT3G13970.

Organism-specific databases

TAIRiAT3G13970.

Phylogenomic databases

eggNOGiKOG3439. Eukaryota.
ENOG4111ND7. LUCA.
HOGENOMiHOG000234863.
InParanoidiQ9LVK3.
KOiK08336.
OMAiIGRISEF.
PhylomeDBiQ9LVK3.

Enzyme and pathway databases

ReactomeiR-ATH-1632852. Macroautophagy.

Miscellaneous databases

EvolutionaryTraceiQ9LVK3.
PROiQ9LVK3.

Family and domain databases

InterProiIPR007242. Atg12.
IPR029071. Ubiquitin-rel_dom.
[Graphical view]
PANTHERiPTHR13385. PTHR13385. 1 hit.
PfamiPF04110. APG12. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene."
    Hanaoka H., Noda T., Shirano Y., Kato T., Hayashi H., Shibata D., Tabata S., Ohsumi Y.
    Plant Physiol. 129:1181-1193(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], NOMENCLATURE, GENE FAMILY.
  2. "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones."
    Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.
    DNA Res. 7:131-135(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Arabidopsis ORF clones."
    Shinn P., Chen H., Kim C.J., Ecker J.R.
    Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "The crystal structure of plant ATG12 and its biological implication in autophagy."
    Suzuki N.N., Yoshimoto K., Fujioka Y., Ohsumi Y., Inagaki F.
    Autophagy 1:119-126(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1-94.
  7. "Autophagic nutrient recycling in Arabidopsis directed by the ATG8 and ATG12 conjugation pathways."
    Thompson A.R., Doelling J.H., Suttangkakul A., Vierstra R.D.
    Plant Physiol. 138:2097-2110(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY.

Entry informationi

Entry nameiAT12B_ARATH
AccessioniPrimary (citable) accession number: Q9LVK3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: October 1, 2000
Last modified: February 17, 2016
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.