APM1_ARATH
ID APM1_ARATH Reviewed; 879 AA.
AC Q8VZH2; Q56WG9; Q9SN00;
DT 11-DEC-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Aminopeptidase M1;
DE EC=3.4.11.2;
DE AltName: Full=Alpha-aminoacylpeptide hydrolase;
GN Name=APM1; OrderedLocusNames=At4g33090; ORFNames=F4I10_20;
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], PROTEIN SEQUENCE OF 161-173 AND 301-314,
RP FUNCTION, BINDING TO NPA, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE,
RP SUBCELLULAR LOCATION, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=cv. Columbia;
RX PubMed=11891249; DOI=10.1104/pp.010519;
RA Murphy A.S., Hoogner K.R., Peer W.A., Taiz L.;
RT "Identification, purification, and molecular cloning of N-1-
RT naphthylphthalmic acid-binding plasma membrane-associated aminopeptidases
RT from Arabidopsis.";
RL Plant Physiol. 128:935-950(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP DISRUPTION PHENOTYPE, FUNCTION, DEVELOPMENTAL STAGE, TISSUE SPECIFICITY,
RP AND SUBCELLULAR LOCATION.
RX PubMed=19531600; DOI=10.1105/tpc.108.059634;
RA Peer W.A., Hosein F.N., Bandyopadhyay A., Makam S.N., Otegui M.S.,
RA Lee G.J., Blakeslee J.J., Cheng Y., Titapiwatanakun B., Yakubov B.,
RA Bangari B., Murphy A.S.;
RT "Mutation of the membrane-associated M1 protease APM1 results in distinct
RT embryonic and seedling developmental defects in Arabidopsis.";
RL Plant Cell 21:1693-1721(2009).
RN [7]
RP SUBUNIT, MOTIFS, MUTAGENESIS OF MET-273; HIS-307 AND LEU-729, AND FUNCTION.
RX PubMed=20154099; DOI=10.1104/pp.109.148742;
RA Hosein F.N., Bandyopadhyay A., Peer W.A., Murphy A.S.;
RT "The catalytic and protein-protein interaction domains are required for
RT APM1 function.";
RL Plant Physiol. 152:2158-2172(2010).
RN [8]
RP SUBCELLULAR LOCATION, AND FUNCTION.
RX PubMed=23065197; DOI=10.1007/s11033-012-1896-1;
RA Lee O.R., Cho H.T.;
RT "Cytoplasm localization of aminopeptidase M1 and its functional activity in
RT root hair cells and BY-2 cells.";
RL Mol. Biol. Rep. 39:10211-10218(2012).
CC -!- FUNCTION: Metallopeptidase that binds to the auxin transport inhibitor
CC N-1-naphthylphthalamic acid (NPA). Required for embryonic and seedling
CC development as well as cell cycle progression. Homodimerization is
CC required to proper localization and activity. May play a negative role
CC in the regulation of PIN auxin transport proteins.
CC {ECO:0000269|PubMed:11891249, ECO:0000269|PubMed:19531600,
CC ECO:0000269|PubMed:20154099, ECO:0000269|PubMed:23065197}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Release of an N-terminal amino acid, Xaa-|-Yaa- from a
CC peptide, amide or arylamide. Xaa is preferably Ala, but may be most
CC amino acids including Pro (slow action). When a terminal hydrophobic
CC residue is followed by a prolyl residue, the two may be released as
CC an intact Xaa-Pro dipeptide.; EC=3.4.11.2;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:11891249};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:11891249};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Vmax=59 nmol/min/mg enzyme for Tyr-aminofluoromethylcoumarin
CC {ECO:0000269|PubMed:11891249};
CC Vmax=35 nmol/min/mg enzyme for Ala-aminofluoromethylcoumarin
CC {ECO:0000269|PubMed:11891249};
CC Vmax=18 nmol/min/mg enzyme for Pro-aminofluoromethylcoumarin
CC {ECO:0000269|PubMed:11891249};
CC -!- SUBUNIT: Homodimer. Interacts with N-1-naphthylphthalamic acid (NPA).
CC {ECO:0000269|PubMed:20154099}.
CC -!- SUBCELLULAR LOCATION: Membrane; Peripheral membrane protein. Microsome
CC membrane; Peripheral membrane protein. Cytoplasm. Note=The dileucine
CC internalization motif may be involved in intracellular sequestration.
CC -!- TISSUE SPECIFICITY: Ubiquitous with preferential expression in 5 days-
CC old seedlings, roots, young flowers, upper inflorescence stems, and
CC rosette leaves. {ECO:0000269|PubMed:11891249,
CC ECO:0000269|PubMed:19531600}.
CC -!- DEVELOPMENTAL STAGE: Expression starts at 3 days and peaks at 5 days.
CC After, expression levels remain constant from 7 to 10 days. During
CC embryogenesis, expressed first at the site of root meristem formation,
CC then in the epidernal and ground tissue, root meristem and suspensor.
CC In the mature embryo, expressed in the vascular primordia throughout
CC the hypocotyl/root axis. {ECO:0000269|PubMed:11891249,
CC ECO:0000269|PubMed:19531600}.
CC -!- DOMAIN: Dileucine motif seems to be involved in protein-protein
CC interactions.
CC -!- DISRUPTION PHENOTYPE: Loss-of-function mutants show irregular,
CC uncoordinated cell divisions throughout embryogenesis, affecting the
CC shape and number of cotyledons and the hypophysis, and is seedling
CC lethal at 5 days after germination due to root growth arrest. Quiescent
CC center and cell cycle markers show no signals in apm1-1 knockdown
CC mutants, and the ground tissue specifiers SHORTROOT and SCARECROW are
CC misexpressed or mislocalized. apm1 mutants have multiple, fused
CC cotyledons and hypocotyls with enlarged epidermal cells with cell
CC adhesion defects. apm1 alleles show defects in gravitropism and auxin
CC transport. {ECO:0000269|PubMed:19531600}.
CC -!- SIMILARITY: Belongs to the peptidase M1 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAD94901.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAB36783.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB80026.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AY143574; AAN41401.1; -; mRNA.
DR EMBL; AL035525; CAB36783.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161582; CAB80026.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE86172.1; -; Genomic_DNA.
DR EMBL; AY064961; AAL38379.1; -; mRNA.
DR EMBL; BT005811; AAO64746.1; -; mRNA.
DR EMBL; AK222071; BAD94901.1; ALT_INIT; mRNA.
DR EMBL; AK227105; BAE99157.1; -; mRNA.
DR PIR; T05189; T05189.
DR RefSeq; NP_195035.2; NM_119463.5.
DR AlphaFoldDB; Q8VZH2; -.
DR SMR; Q8VZH2; -.
DR BioGRID; 14731; 31.
DR IntAct; Q8VZH2; 1.
DR STRING; 3702.AT4G33090.1; -.
DR MEROPS; M01.A25; -.
DR PaxDb; Q8VZH2; -.
DR PRIDE; Q8VZH2; -.
DR ProMEX; Q8VZH2; -.
DR ProteomicsDB; 244964; -.
DR EnsemblPlants; AT4G33090.1; AT4G33090.1; AT4G33090.
DR GeneID; 829446; -.
DR Gramene; AT4G33090.1; AT4G33090.1; AT4G33090.
DR KEGG; ath:AT4G33090; -.
DR Araport; AT4G33090; -.
DR TAIR; locus:2125904; AT4G33090.
DR eggNOG; KOG1046; Eukaryota.
DR HOGENOM; CLU_003705_0_1_1; -.
DR InParanoid; Q8VZH2; -.
DR OMA; MMEYVAI; -.
DR OrthoDB; 110058at2759; -.
DR PhylomeDB; Q8VZH2; -.
DR PRO; PR:Q8VZH2; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8VZH2; baseline and differential.
DR Genevisible; Q8VZH2; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005783; C:endoplasmic reticulum; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IDA:TAIR.
DR GO; GO:0004177; F:aminopeptidase activity; IDA:TAIR.
DR GO; GO:0070006; F:metalloaminopeptidase activity; IBA:GO_Central.
DR GO; GO:0010013; F:N-1-naphthylphthalamic acid binding; IDA:UniProtKB.
DR GO; GO:0042277; F:peptide binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IBA:GO_Central.
DR GO; GO:0009926; P:auxin polar transport; TAS:TAIR.
DR GO; GO:0043171; P:peptide catabolic process; IBA:GO_Central.
DR GO; GO:0006508; P:proteolysis; IBA:GO_Central.
DR CDD; cd09601; M1_APN-Q_like; 1.
DR Gene3D; 1.10.390.10; -; 1.
DR Gene3D; 2.60.40.1730; -; 1.
DR InterPro; IPR045357; Aminopeptidase_N-like_N.
DR InterPro; IPR042097; Aminopeptidase_N-like_N_sf.
DR InterPro; IPR024571; ERAP1-like_C_dom.
DR InterPro; IPR034016; M1_APN-typ.
DR InterPro; IPR001930; Peptidase_M1.
DR InterPro; IPR014782; Peptidase_M1_dom.
DR InterPro; IPR027268; Peptidase_M4/M1_CTD_sf.
DR Pfam; PF11838; ERAP1_C; 1.
DR Pfam; PF01433; Peptidase_M1; 1.
DR Pfam; PF17900; Peptidase_M1_N; 1.
DR PRINTS; PR00756; ALADIPTASE.
DR SUPFAM; SSF63737; SSF63737; 1.
DR PROSITE; PS00142; ZINC_PROTEASE; 1.
PE 1: Evidence at protein level;
KW Aminopeptidase; Cytoplasm; Direct protein sequencing;
KW Endoplasmic reticulum; Hydrolase; Membrane; Metal-binding; Metalloprotease;
KW Microsome; Protease; Reference proteome; Zinc.
FT CHAIN 1..879
FT /note="Aminopeptidase M1"
FT /id="PRO_0000424583"
FT REGION 98..205
FT /note="Required for membrane association"
FT MOTIF 728..729
FT /note="Dileucine internalization motif"
FT /evidence="ECO:0000255"
FT ACT_SITE 308
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT BINDING 138
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 271..275
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 307
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT BINDING 311
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT BINDING 330
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT SITE 392
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT MUTAGEN 273
FT /note="M->K: Abolishes function."
FT /evidence="ECO:0000269|PubMed:20154099"
FT MUTAGEN 307
FT /note="H->A: Abolishes function."
FT /evidence="ECO:0000269|PubMed:20154099"
FT MUTAGEN 729
FT /note="L->A: Decreases protein stability and abolishes
FT function."
FT /evidence="ECO:0000269|PubMed:20154099"
SQ SEQUENCE 879 AA; 98179 MW; 9E7E6D7E8F5AB991 CRC64;
MDQFKGEPRL PKFAVPKRYD LRLNPDLIAC TFTGTVAIDL DIVADTRFIV LNAADLSVND
ASVSFTPPSS SKALAAPKVV LFEEDEILVL EFGEILPHGV GVLKLGFNGV LNDKMKGFYR
STYEHNGEKK NMAVTQFEPA DARRCFPCWD EPACKATFKI TLEVPTDLVA LSNMPIMEEK
VNGNLKIVSY QESPIMSTYL VAIVVGLFDY VEDHTSDGIK VRVYCQVGKA DQGKFALHVG
AKTLDLFKEY FAVPYPLPKM DMIAIPDFAA GAMENYGLVT YRETALLYDE QHSAASNKQR
VATVVAHELA HQWFGNLVTM EWWTHLWLNE GFATWVSYLA TDSLFPEWKI WTQFLDESTE
GLRLDGLEES HPIEVEVNHA AEIDEIFDAI SYRKGASVIR MLQSYLGAEV FQKSLAAYIK
NHAYSNAKTE DLWAALEAGS GEPVNKLMSS WTKQKGYPVV SAKIKDGKLE LEQSRFLSSG
SPGEGQWIVP VTLCCGSYEK RKNFLLESKS GAYDLKELLG CSIADGSDKI NGTCSWIKIN
VDQAGFYRVK YDDSLAAGLR NATESQSLTS IDRYGILDDS FALTMARQQS LASLLTLCSA
YKKELDYTVL SNLIAISYKV VKIGADANQE LMSGIKHFFI GVFQFAAGKL GWDPKQGESH
LDAMLRGEVL TALAVFGHDE TLKEAVRRFD AFLADRNTPL LPPDIRRAAY VAVMQRANKS
DKSGYESLLR VYRETDLSQE KTRILGSLAS CPDPTIVQDV LNFVLSDEVR NQDALYGLSG
VSWEGREVAW KWLQEKWEYI GNTWGSGFLI TRFISAVVSP FASFEKAKEV EEFFATRSKP
SMARTLKQSI ERVHINANWV ESIKKEDNLT QLVAQLSSN
