PEX4_ARATH
ID PEX4_ARATH Reviewed; 157 AA.
AC Q8LGF7;
DT 22-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Protein PEROXIN-4;
DE Short=AtPEX4;
DE AltName: Full=E2 ubiquitin-conjugating enzyme 21;
DE AltName: Full=Probable ubiquitin-conjugating enzyme E2 21;
DE EC=2.3.2.23;
DE AltName: Full=Ubiquitin carrier protein 21;
GN Name=PEX4; Synonyms=UBC21; OrderedLocusNames=At5g25760; ORFNames=F18A17.10;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16339806; DOI=10.1104/pp.105.067983;
RA Kraft E., Stone S.L., Ma L., Su N., Gao Y., Lau O.-S., Deng X.-W.,
RA Callis J.;
RT "Genome analysis and functional characterization of the E2 and RING-type E3
RT ligase ubiquitination enzymes of Arabidopsis.";
RL Plant Physiol. 139:1597-1611(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Quinitio C., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP IDENTIFICATION, MUTAGENESIS OF PRO-123, AND INTERACTION WITH PEX22.
RX PubMed=16272432; DOI=10.1105/tpc.105.035691;
RA Zolman B.K., Monroe-Augustus M., Silva I.D., Bartel B.;
RT "Identification and functional characterization of Arabidopsis PEROXIN4 and
RT the interacting protein PEROXIN22.";
RL Plant Cell 17:3422-3435(2005).
RN [7]
RP FUNCTION.
RX PubMed=17478547; DOI=10.1093/pcp/pcm053;
RA Nito K., Kamigaki A., Kondo M., Hayashi M., Nishimura M.;
RT "Functional classification of Arabidopsis peroxisome biogenesis factors
RT proposed from analyses of knockdown mutants.";
RL Plant Cell Physiol. 48:763-774(2007).
RN [8]
RP FUNCTION.
RX PubMed=19246395; DOI=10.1073/pnas.0811329106;
RA Lingard M.J., Monroe-Augustus M., Bartel B.;
RT "Peroxisome-associated matrix protein degradation in Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:4561-4566(2009).
CC -!- FUNCTION: Required for peroxisome biogenesis. Necessary for the
CC developmental elimination of obsolete peroxisome matrix proteins. May
CC be involved in the ubiquitination of PEX5, targeting it for recycling.
CC Accepts the ubiquitin from the E1 complex and catalyzes its covalent
CC attachment to other proteins. {ECO:0000250,
CC ECO:0000269|PubMed:17478547, ECO:0000269|PubMed:19246395}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine +
CC [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-
CC activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-
CC conjugating enzyme]-L-cysteine.; EC=2.3.2.23;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00388, ECO:0000255|PROSITE-
CC ProRule:PRU10133};
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC {ECO:0000255|PROSITE-ProRule:PRU00388}.
CC -!- SUBUNIT: Interacts with PEX22. {ECO:0000269|PubMed:16272432}.
CC -!- SUBCELLULAR LOCATION: Peroxisome membrane
CC {ECO:0000250|UniProtKB:P29340}; Peripheral membrane protein
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the ubiquitin-conjugating enzyme family.
CC {ECO:0000255|PROSITE-ProRule:PRU00388}.
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DR EMBL; DQ027035; AAY44861.1; -; mRNA.
DR EMBL; AC005405; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED93482.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93483.1; -; Genomic_DNA.
DR EMBL; AY084297; AAM60888.1; -; mRNA.
DR EMBL; BT025616; ABF59034.1; -; mRNA.
DR RefSeq; NP_001031939.1; NM_001036862.2.
DR RefSeq; NP_568476.1; NM_122477.2.
DR PDB; 6XOD; X-ray; 2.01 A; A=1-157.
DR PDBsum; 6XOD; -.
DR AlphaFoldDB; Q8LGF7; -.
DR SMR; Q8LGF7; -.
DR BioGRID; 17920; 1.
DR IntAct; Q8LGF7; 1.
DR STRING; 3702.AT5G25760.2; -.
DR PaxDb; Q8LGF7; -.
DR PRIDE; Q8LGF7; -.
DR ProteomicsDB; 251199; -.
DR EnsemblPlants; AT5G25760.1; AT5G25760.1; AT5G25760.
DR EnsemblPlants; AT5G25760.2; AT5G25760.2; AT5G25760.
DR GeneID; 832645; -.
DR Gramene; AT5G25760.1; AT5G25760.1; AT5G25760.
DR Gramene; AT5G25760.2; AT5G25760.2; AT5G25760.
DR KEGG; ath:AT5G25760; -.
DR Araport; AT5G25760; -.
DR TAIR; locus:2145269; AT5G25760.
DR eggNOG; KOG0417; Eukaryota.
DR HOGENOM; CLU_030988_13_0_1; -.
DR OMA; PIKRLMT; -.
DR OrthoDB; 1412570at2759; -.
DR PhylomeDB; Q8LGF7; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q8LGF7; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8LGF7; baseline and differential.
DR Genevisible; Q8LGF7; AT.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005778; C:peroxisomal membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0061631; F:ubiquitin conjugating enzyme activity; IBA:GO_Central.
DR GO; GO:0004842; F:ubiquitin-protein transferase activity; ISS:TAIR.
DR GO; GO:0006635; P:fatty acid beta-oxidation; IMP:TAIR.
DR GO; GO:0007031; P:peroxisome organization; IMP:TAIR.
DR GO; GO:0016558; P:protein import into peroxisome matrix; IMP:TAIR.
DR GO; GO:0000209; P:protein polyubiquitination; IBA:GO_Central.
DR GO; GO:0016567; P:protein ubiquitination; IDA:TAIR.
DR CDD; cd00195; UBCc; 1.
DR Gene3D; 3.10.110.10; -; 1.
DR InterPro; IPR000608; UBQ-conjugat_E2.
DR InterPro; IPR023313; UBQ-conjugating_AS.
DR InterPro; IPR016135; UBQ-conjugating_enzyme/RWD.
DR Pfam; PF00179; UQ_con; 1.
DR SUPFAM; SSF54495; SSF54495; 1.
DR PROSITE; PS00183; UBC_1; 1.
DR PROSITE; PS50127; UBC_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Membrane; Nucleotide-binding; Peroxisome;
KW Peroxisome biogenesis; Protein transport; Reference proteome; Transferase;
KW Transport; Ubl conjugation pathway.
FT CHAIN 1..157
FT /note="Protein PEROXIN-4"
FT /id="PRO_0000345187"
FT DOMAIN 3..153
FT /note="UBC core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00388"
FT ACT_SITE 90
FT /note="Glycyl thioester intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00388,
FT ECO:0000255|PROSITE-ProRule:PRU10133"
FT MUTAGEN 123
FT /note="P->L: In pex4-1; reduced peroxisomal function and
FT loss of response to indole-3-butyric acid."
FT /evidence="ECO:0000269|PubMed:16272432"
FT HELIX 2..16
FT /evidence="ECO:0007829|PDB:6XOD"
FT STRAND 25..29
FT /evidence="ECO:0007829|PDB:6XOD"
FT STRAND 36..42
FT /evidence="ECO:0007829|PDB:6XOD"
FT TURN 48..51
FT /evidence="ECO:0007829|PDB:6XOD"
FT STRAND 53..59
FT /evidence="ECO:0007829|PDB:6XOD"
FT TURN 62..65
FT /evidence="ECO:0007829|PDB:6XOD"
FT STRAND 70..75
FT /evidence="ECO:0007829|PDB:6XOD"
FT TURN 84..86
FT /evidence="ECO:0007829|PDB:6XOD"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:6XOD"
FT HELIX 104..116
FT /evidence="ECO:0007829|PDB:6XOD"
FT STRAND 120..122
FT /evidence="ECO:0007829|PDB:6XOD"
FT HELIX 126..133
FT /evidence="ECO:0007829|PDB:6XOD"
FT HELIX 137..151
FT /evidence="ECO:0007829|PDB:6XOD"
SQ SEQUENCE 157 AA; 17708 MW; 36FB1E11684F48B4 CRC64;
MQASRARLFK EYKEVQREKV ADPDIQLICD DTNIFKWTAL IKGPSETPYE GGVFQLAFSV
PEPYPLQPPQ VRFLTKIFHP NVHFKTGEIC LDILKNAWSP AWTLQSVCRA IIALMAHPEP
DSPLNCDSGN LLRSGDVRGF NSMAQMYTRL AAMPKKG
