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Protein

Protein PEROXIN-4

Gene

PEX4

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

Functioni

Required for peroxisome biogenesis. Necessary for the developmental elimination of obsolete peroxisome matrix proteins. May be involved in the ubiquitination of PEX5, targeting it for recycling. Accepts the ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins (By similarity).By similarity

Catalytic activityi

ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.PROSITE-ProRule annotation

Pathway:iprotein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.PROSITE-ProRule annotation
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei90 – 901Glycyl thioester intermediatePROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

  • fatty acid beta-oxidation Source: TAIR
  • peroxisome organization Source: TAIR
  • protein import into peroxisome matrix Source: TAIR
  • protein ubiquitination Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Peroxisome biogenesis, Protein transport, Transport, Ubl conjugation pathway

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciARA:AT5G25760-MONOMER.
ARA:GQT-755-MONOMER.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein PEROXIN-4
Short name:
AtPEX4
Alternative name(s):
Probable ubiquitin-conjugating enzyme E2 21 (EC:6.3.2.19)
Ubiquitin carrier protein 21
Gene namesi
Name:PEX4
Synonyms:UBC21
Ordered Locus Names:At5g25760
ORF Names:F18A17.10
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G25760.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane, Peroxisome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi123 – 1231P → L in pex4-1; reduced peroxisomal function and loss of response to indole-3-butyric acid. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 157157Protein PEROXIN-4PRO_0000345187Add
BLAST

Proteomic databases

PaxDbiQ8LGF7.
PRIDEiQ8LGF7.

Interactioni

Subunit structurei

Interacts with PEX22.1 Publication

Protein-protein interaction databases

BioGridi17920. 1 interaction.
IntActiQ8LGF7. 1 interaction.
STRINGi3702.AT5G25760.1.

Structurei

3D structure databases

ProteinModelPortaliQ8LGF7.
SMRiQ8LGF7. Positions 7-127.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ubiquitin-conjugating enzyme family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG5078.
HOGENOMiHOG000233455.
KOiK10689.
OMAiHPNIHFK.
PhylomeDBiQ8LGF7.

Family and domain databases

Gene3Di3.10.110.10. 1 hit.
InterProiIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamiPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMiSSF54495. SSF54495. 1 hit.
PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8LGF7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQASRARLFK EYKEVQREKV ADPDIQLICD DTNIFKWTAL IKGPSETPYE
60 70 80 90 100
GGVFQLAFSV PEPYPLQPPQ VRFLTKIFHP NVHFKTGEIC LDILKNAWSP
110 120 130 140 150
AWTLQSVCRA IIALMAHPEP DSPLNCDSGN LLRSGDVRGF NSMAQMYTRL

AAMPKKG
Length:157
Mass (Da):17,708
Last modified:October 1, 2002 - v1
Checksum:i36FB1E11684F48B4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ027035 mRNA. Translation: AAY44861.1.
AC005405 Genomic DNA. No translation available.
CP002688 Genomic DNA. Translation: AED93482.1.
CP002688 Genomic DNA. Translation: AED93483.1.
AY084297 mRNA. Translation: AAM60888.1.
BT025616 mRNA. Translation: ABF59034.1.
RefSeqiNP_001031939.1. NM_001036862.1.
NP_568476.1. NM_122477.2.
UniGeneiAt.20548.
At.30893.

Genome annotation databases

EnsemblPlantsiAT5G25760.1; AT5G25760.1; AT5G25760.
AT5G25760.2; AT5G25760.2; AT5G25760.
GeneIDi832645.
KEGGiath:AT5G25760.

Cross-referencesi

Web resourcesi

PlantsUBQ

A functional genomics database for the ubiquitin/26S proteasome proteolytic pathway in plants

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ027035 mRNA. Translation: AAY44861.1.
AC005405 Genomic DNA. No translation available.
CP002688 Genomic DNA. Translation: AED93482.1.
CP002688 Genomic DNA. Translation: AED93483.1.
AY084297 mRNA. Translation: AAM60888.1.
BT025616 mRNA. Translation: ABF59034.1.
RefSeqiNP_001031939.1. NM_001036862.1.
NP_568476.1. NM_122477.2.
UniGeneiAt.20548.
At.30893.

3D structure databases

ProteinModelPortaliQ8LGF7.
SMRiQ8LGF7. Positions 7-127.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi17920. 1 interaction.
IntActiQ8LGF7. 1 interaction.
STRINGi3702.AT5G25760.1.

Proteomic databases

PaxDbiQ8LGF7.
PRIDEiQ8LGF7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G25760.1; AT5G25760.1; AT5G25760.
AT5G25760.2; AT5G25760.2; AT5G25760.
GeneIDi832645.
KEGGiath:AT5G25760.

Organism-specific databases

TAIRiAT5G25760.

Phylogenomic databases

eggNOGiCOG5078.
HOGENOMiHOG000233455.
KOiK10689.
OMAiHPNIHFK.
PhylomeDBiQ8LGF7.

Enzyme and pathway databases

UniPathwayiUPA00143.
BioCyciARA:AT5G25760-MONOMER.
ARA:GQT-755-MONOMER.

Miscellaneous databases

PROiQ8LGF7.

Family and domain databases

Gene3Di3.10.110.10. 1 hit.
InterProiIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamiPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMiSSF54495. SSF54495. 1 hit.
PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Genome analysis and functional characterization of the E2 and RING-type E3 ligase ubiquitination enzymes of Arabidopsis."
    Kraft E., Stone S.L., Ma L., Su N., Gao Y., Lau O.-S., Deng X.-W., Callis J.
    Plant Physiol. 139:1597-1611(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], GENE FAMILY, NOMENCLATURE.
  2. "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
    Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.
    , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
    Nature 408:823-826(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. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  5. "Arabidopsis ORF clones."
    Quinitio C., Chen H., Kim C.J., Shinn P., Ecker J.R.
    Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "Identification and functional characterization of Arabidopsis PEROXIN4 and the interacting protein PEROXIN22."
    Zolman B.K., Monroe-Augustus M., Silva I.D., Bartel B.
    Plant Cell 17:3422-3435(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION, MUTAGENESIS OF PRO-123, INTERACTION WITH PEX22.
  7. "Functional classification of Arabidopsis peroxisome biogenesis factors proposed from analyses of knockdown mutants."
    Nito K., Kamigaki A., Kondo M., Hayashi M., Nishimura M.
    Plant Cell Physiol. 48:763-774(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Peroxisome-associated matrix protein degradation in Arabidopsis."
    Lingard M.J., Monroe-Augustus M., Bartel B.
    Proc. Natl. Acad. Sci. U.S.A. 106:4561-4566(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiPEX4_ARATH
AccessioniPrimary (citable) accession number: Q8LGF7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 22, 2008
Last sequence update: October 1, 2002
Last modified: July 22, 2015
This is version 100 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

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.