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Calpain-type cysteine protease DEK1 (EC 3.4.22.-) (Phytocalpain DEK1) (Protein DEFECTIVE KERNEL 1) (ZmDEK1)

 DEK1_MAIZE              Reviewed;        2159 AA.
Q8RVL1; B4FFL6;
18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
18-SEP-2013, sequence version 2.
27-SEP-2017, entry version 87.
RecName: Full=Calpain-type cysteine protease DEK1;
EC=3.4.22.-;
AltName: Full=Phytocalpain DEK1;
AltName: Full=Protein DEFECTIVE KERNEL 1;
Short=ZmDEK1;
Flags: Precursor;
Name=DEK1;
Zea mays (Maize).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae;
PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae;
Zea.
NCBI_TaxID=4577;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, DISRUPTION
PHENOTYPE, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
STRAIN=cv. B73; TISSUE=Endosperm;
PubMed=11929961; DOI=10.1073/pnas.042098799;
Lid S.E., Gruis D., Jung R., Lorentzen J.A., Ananiev E.,
Chamberlin M., Niu X., Meeley R., Nichols S., Olsen O.-A.;
"The defective kernel 1 (dek1) gene required for aleurone cell
development in the endosperm of maize grains encodes a membrane
protein of the calpain gene superfamily.";
Proc. Natl. Acad. Sci. U.S.A. 99:5460-5465(2002).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. B73;
PubMed=19965430; DOI=10.1126/science.1178534;
Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S.,
Liang C., Zhang J., Fulton L., Graves T.A., Minx P., Reily A.D.,
Courtney L., Kruchowski S.S., Tomlinson C., Strong C., Delehaunty K.,
Fronick C., Courtney B., Rock S.M., Belter E., Du F., Kim K.,
Abbott R.M., Cotton M., Levy A., Marchetto P., Ochoa K., Jackson S.M.,
Gillam B., Chen W., Yan L., Higginbotham J., Cardenas M.,
Waligorski J., Applebaum E., Phelps L., Falcone J., Kanchi K.,
Thane T., Scimone A., Thane N., Henke J., Wang T., Ruppert J.,
Shah N., Rotter K., Hodges J., Ingenthron E., Cordes M., Kohlberg S.,
Sgro J., Delgado B., Mead K., Chinwalla A., Leonard S., Crouse K.,
Collura K., Kudrna D., Currie J., He R., Angelova A., Rajasekar S.,
Mueller T., Lomeli R., Scara G., Ko A., Delaney K., Wissotski M.,
Lopez G., Campos D., Braidotti M., Ashley E., Golser W., Kim H.,
Lee S., Lin J., Dujmic Z., Kim W., Talag J., Zuccolo A., Fan C.,
Sebastian A., Kramer M., Spiegel L., Nascimento L., Zutavern T.,
Miller B., Ambroise C., Muller S., Spooner W., Narechania A., Ren L.,
Wei S., Kumari S., Faga B., Levy M.J., McMahan L., Van Buren P.,
Vaughn M.W., Ying K., Yeh C.-T., Emrich S.J., Jia Y., Kalyanaraman A.,
Hsia A.-P., Barbazuk W.B., Baucom R.S., Brutnell T.P., Carpita N.C.,
Chaparro C., Chia J.-M., Deragon J.-M., Estill J.C., Fu Y.,
Jeddeloh J.A., Han Y., Lee H., Li P., Lisch D.R., Liu S., Liu Z.,
Nagel D.H., McCann M.C., SanMiguel P., Myers A.M., Nettleton D.,
Nguyen J., Penning B.W., Ponnala L., Schneider K.L., Schwartz D.C.,
Sharma A., Soderlund C., Springer N.M., Sun Q., Wang H., Waterman M.,
Westerman R., Wolfgruber T.K., Yang L., Yu Y., Zhang L., Zhou S.,
Zhu Q., Bennetzen J.L., Dawe R.K., Jiang J., Jiang N., Presting G.G.,
Wessler S.R., Aluru S., Martienssen R.A., Clifton S.W., McCombie W.R.,
Wing R.A., Wilson R.K.;
"The B73 maize genome: complexity, diversity, and dynamics.";
Science 326:1112-1115(2009).
[3]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
STRAIN=cv. B73;
PubMed=19936069; DOI=10.1371/journal.pgen.1000740;
Soderlund C., Descour A., Kudrna D., Bomhoff M., Boyd L., Currie J.,
Angelova A., Collura K., Wissotski M., Ashley E., Morrow D.,
Fernandes J., Walbot V., Yu Y.;
"Sequencing, mapping, and analysis of 27,455 maize full-length
cDNAs.";
PLoS Genet. 5:E1000740-E1000740(2009).
[4]
FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF CYS-1769, AND TISSUE
SPECIFICITY.
PubMed=12824178; DOI=10.1074/jbc.M300745200;
Wang C., Barry J.K., Min Z., Tordsen G., Rao A.G., Olsen O.A.;
"The calpain domain of the maize DEK1 protein contains the conserved
catalytic triad and functions as a cysteine proteinase.";
J. Biol. Chem. 278:34467-34474(2003).
[5]
FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
PubMed=17933905; DOI=10.1105/tpc.106.048868;
Tian Q., Olsen L., Sun B., Lid S.E., Brown R.C., Lemmon B.E.,
Fosnes K., Gruis D.F., Opsahl-Sorteberg H.-G., Otegui M.S.,
Olsen O.-A.;
"Subcellular localization and functional domain studies of DEFECTIVE
KERNEL1 in maize and Arabidopsis suggest a model for aleurone cell
fate specification involving CRINKLY4 and SUPERNUMERARY ALEURONE
LAYER1.";
Plant Cell 19:3127-3145(2007).
-!- FUNCTION: Essential protein involved in epiderm development.
Required for aleurone cell development in the endosperm probably
by maintaining and restricting the aleurone and embryonic
epidermal L1 cell-layer fates as well as meristems organization.
Involved in the maintenance of adaxial/abaxial axis information in
developing leaves, probably by regulating cell proliferation and
expansion. Does not need calcium ions to be active.
{ECO:0000269|PubMed:11929961, ECO:0000269|PubMed:12824178,
ECO:0000269|PubMed:17933905}.
-!- CATALYTIC ACTIVITY: Broad endopeptidase specificity.
{ECO:0000269|PubMed:12824178}.
-!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
{ECO:0000250}; Multi-pass membrane protein {ECO:0000250}.
Cytoplasm {ECO:0000250}. Cell membrane
{ECO:0000269|PubMed:17933905}; Multi-pass membrane protein
{ECO:0000269|PubMed:17933905}. Endosome membrane
{ECO:0000269|PubMed:17933905}; Multi-pass membrane protein
{ECO:0000269|PubMed:17933905}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q8RVL1-1; Sequence=Displayed;
Name=2;
IsoId=Q8RVL1-2; Sequence=VSP_047871;
-!- TISSUE SPECIFICITY: Expressed in most tissues at low levels
ranging from 30 to 55 ppm. Present in all endosperm cells at
transcript level, but confined to aleurones at protein level.
{ECO:0000269|PubMed:11929961, ECO:0000269|PubMed:12824178}.
-!- DEVELOPMENTAL STAGE: In endosperm, accumulates during early
developmental stages and declines near maturity. In embryos,
levels peak at middevelopment with highest expression in the
embryonic axis. Also present in young pericarp and immature ear
tip and base. {ECO:0000269|PubMed:11929961}.
-!- DOMAIN: The transmembrane regions are not required for calpain
activity but may play regulatory roles. {ECO:0000250}.
-!- PTM: Autocatalytic proteolytic cleavage leading to the production
of mainly cytoplasmic localized subproducts of about 85 and 120
kDa. {ECO:0000250}.
-!- DISRUPTION PHENOTYPE: Loss of aleurone cells leading to white
grains. Embryos arrest at the juvenile globoid stage and are
devoid of shoot structures. {ECO:0000269|PubMed:11929961,
ECO:0000269|PubMed:17933905}.
-!- MISCELLANEOUS: Although homology to other calpains is high within
the protease domain, the lack of calcium-binding sites suggests
that this protein is a protease that may not be activated by
calcium ions. {ECO:0000250}.
-!- SIMILARITY: Belongs to the peptidase C2 family. {ECO:0000305}.
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EMBL; AY061806; AAL38189.1; -; mRNA.
EMBL; CM007647; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; BT035904; ACF80909.1; -; mRNA.
RefSeq; NP_001105528.1; NM_001112058.1.
RefSeq; XP_008648830.1; XM_008650608.1.
UniGene; Zm.95757; -.
SMR; Q8RVL1; -.
STRING; 4577.GRMZM2G321753_P01; -.
MEROPS; C02.019; -.
PaxDb; Q8RVL1; -.
EnsemblPlants; Zm00001d028818_T053; Zm00001d028818_P053; Zm00001d028818. [Q8RVL1-2]
EnsemblPlants; Zm00001d028818_T057; Zm00001d028818_P057; Zm00001d028818. [Q8RVL1-2]
GeneID; 542509; -.
Gramene; Zm00001d028818_T053; Zm00001d028818_P053; Zm00001d028818.
Gramene; Zm00001d028818_T057; Zm00001d028818_P057; Zm00001d028818.
KEGG; zma:542509; -.
MaizeGDB; 12148; -.
eggNOG; KOG0045; Eukaryota.
eggNOG; ENOG410XP0B; LUCA.
Proteomes; UP000007305; Chromosome 1.
GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
GO; GO:0005789; C:endoplasmic reticulum membrane; ISS:UniProtKB.
GO; GO:0010008; C:endosome membrane; IDA:UniProtKB.
GO; GO:0005887; C:integral component of plasma membrane; IDA:UniProtKB.
GO; GO:0004198; F:calcium-dependent cysteine-type endopeptidase activity; IEA:InterPro.
GO; GO:0008234; F:cysteine-type peptidase activity; IMP:UniProtKB.
GO; GO:0009793; P:embryo development ending in seed dormancy; ISS:UniProtKB.
GO; GO:0090628; P:plant epidermal cell fate specification; ISS:UniProtKB.
GO; GO:2000011; P:regulation of adaxial/abaxial pattern formation; ISS:UniProtKB.
GO; GO:0001558; P:regulation of cell growth; ISS:UniProtKB.
GO; GO:0042127; P:regulation of cell proliferation; ISS:UniProtKB.
GO; GO:2000014; P:regulation of endosperm development; ISS:UniProtKB.
GO; GO:2000024; P:regulation of leaf development; ISS:UniProtKB.
GO; GO:0009934; P:regulation of meristem structural organization; ISS:UniProtKB.
GO; GO:0097264; P:self proteolysis; ISS:UniProtKB.
CDD; cd00044; CysPc; 1.
InterPro; IPR022682; Calpain_domain_III.
InterPro; IPR022683; Calpain_III.
InterPro; IPR013320; ConA-like_dom.
InterPro; IPR000169; Pept_cys_AS.
InterPro; IPR001300; Peptidase_C2_calpain_cat.
Pfam; PF01067; Calpain_III; 1.
Pfam; PF00648; Peptidase_C2; 1.
SMART; SM00720; calpain_III; 1.
SMART; SM00230; CysPc; 1.
SUPFAM; SSF49758; SSF49758; 1.
SUPFAM; SSF49899; SSF49899; 1.
PROSITE; PS50203; CALPAIN_CAT; 1.
PROSITE; PS00139; THIOL_PROTEASE_CYS; 1.
1: Evidence at protein level;
Alternative splicing; Cell membrane; Complete proteome; Cytoplasm;
Developmental protein; Endoplasmic reticulum; Endosome; Hydrolase;
Membrane; Phosphoprotein; Protease; Reference proteome; Repeat;
Signal; Thiol protease; Transmembrane; Transmembrane helix.
SIGNAL 1 33 {ECO:0000255}.
CHAIN 34 2159 Calpain-type cysteine protease DEK1.
/FTId=PRO_0000423439.
PROPEP 34 ? {ECO:0000250}.
/FTId=PRO_0000423440.
TOPO_DOM 34 70 Extracellular. {ECO:0000255}.
TRANSMEM 71 91 Helical; Name=1. {ECO:0000255}.
TOPO_DOM 92 95 Cytoplasmic. {ECO:0000255}.
TRANSMEM 96 116 Helical; Name=2. {ECO:0000255}.
TOPO_DOM 117 127 Extracellular. {ECO:0000255}.
TRANSMEM 128 148 Helical; Name=3. {ECO:0000255}.
TOPO_DOM 149 164 Cytoplasmic. {ECO:0000255}.
TRANSMEM 165 185 Helical; Name=4. {ECO:0000255}.
TOPO_DOM 186 236 Extracellular. {ECO:0000255}.
TRANSMEM 237 257 Helical; Name=5. {ECO:0000255}.
TOPO_DOM 258 264 Cytoplasmic. {ECO:0000255}.
TRANSMEM 265 285 Helical; Name=6. {ECO:0000255}.
TOPO_DOM 286 294 Extracellular. {ECO:0000255}.
TRANSMEM 295 315 Helical; Name=7. {ECO:0000255}.
TOPO_DOM 316 320 Cytoplasmic. {ECO:0000255}.
TRANSMEM 321 341 Helical; Name=8. {ECO:0000255}.
TOPO_DOM 342 623 Extracellular. {ECO:0000255}.
TRANSMEM 624 644 Helical; Name=9. {ECO:0000255}.
TOPO_DOM 645 660 Cytoplasmic. {ECO:0000255}.
TRANSMEM 661 681 Helical; Name=10. {ECO:0000255}.
TOPO_DOM 682 694 Extracellular. {ECO:0000255}.
TRANSMEM 695 715 Helical; Name=11. {ECO:0000255}.
TOPO_DOM 716 719 Cytoplasmic. {ECO:0000255}.
TRANSMEM 720 740 Helical; Name=12. {ECO:0000255}.
TOPO_DOM 741 770 Extracellular. {ECO:0000255}.
TRANSMEM 771 791 Helical; Name=13. {ECO:0000255}.
TOPO_DOM 792 822 Cytoplasmic. {ECO:0000255}.
TRANSMEM 823 843 Helical; Name=14. {ECO:0000255}.
TOPO_DOM 844 853 Extracellular. {ECO:0000255}.
TRANSMEM 854 874 Helical; Name=15. {ECO:0000255}.
TOPO_DOM 875 887 Cytoplasmic. {ECO:0000255}.
TRANSMEM 888 908 Helical; Name=16. {ECO:0000255}.
TOPO_DOM 909 921 Extracellular. {ECO:0000255}.
TRANSMEM 922 942 Helical; Name=17. {ECO:0000255}.
TOPO_DOM 943 946 Cytoplasmic. {ECO:0000255}.
TRANSMEM 947 967 Helical; Name=18. {ECO:0000255}.
TOPO_DOM 968 981 Extracellular. {ECO:0000255}.
TRANSMEM 982 1002 Helical; Name=19. {ECO:0000255}.
TOPO_DOM 1003 1016 Cytoplasmic. {ECO:0000255}.
TRANSMEM 1017 1037 Helical; Name=20. {ECO:0000255}.
TOPO_DOM 1038 1060 Extracellular. {ECO:0000255}.
TRANSMEM 1061 1081 Helical; Name=21. {ECO:0000255}.
TOPO_DOM 1082 2159 Cytoplasmic. {ECO:0000255}.
DOMAIN 1417 1609 Calpain catalytic 1.
{ECO:0000255|PROSITE-ProRule:PRU00239}.
DOMAIN 1703 2005 Calpain catalytic 2.
{ECO:0000255|PROSITE-ProRule:PRU00239}.
COMPBIAS 370 493 Ser-rich.
COMPBIAS 1248 1254 Poly-Leu.
ACT_SITE 1769 1769 {ECO:0000250}.
ACT_SITE 1927 1927 {ECO:0000250}.
ACT_SITE 1947 1947 {ECO:0000250}.
MOD_RES 1371 1371 Phosphoserine. {ECO:0000250}.
MOD_RES 1376 1376 Phosphoserine. {ECO:0000250}.
MOD_RES 1665 1665 Phosphoserine. {ECO:0000250}.
VAR_SEQ 1 1877 Missing (in isoform 2).
{ECO:0000303|PubMed:11929961,
ECO:0000303|PubMed:19936069}.
/FTId=VSP_047871.
MUTAGEN 1769 1769 C->S: Loss of activity.
{ECO:0000269|PubMed:12824178}.
CONFLICT 92 92 M -> L (in Ref. 1; AAL38189).
{ECO:0000305}.
CONFLICT 127 127 E -> K (in Ref. 1; AAL38189).
{ECO:0000305}.
CONFLICT 138 138 C -> G (in Ref. 1; AAL38189).
{ECO:0000305}.
CONFLICT 398 398 M -> T (in Ref. 1; AAL38189).
{ECO:0000305}.
CONFLICT 469 469 I -> T (in Ref. 1; AAL38189).
{ECO:0000305}.
SEQUENCE 2159 AA; 239106 MW; 041D8974E4BA0AA5 CRC64;
MEGEGHHGVV LACSICGFLF AVLSPFSFWV LWAVNWRPWR LYSWIYARKW PTYVQGPQLS
TLCSLLTLCA WLVVISPIAV LLVWGSVLIA LMERNIIGLA VIMAGVALLL SFYSIMLWWR
TQWQSSEAVA YLLLLAVCLL CAYDFCAIYV TAGASASELN SPSGFFFGVS VISLAINMLF
ICKILFNVSG FDVDEYVRRS YKFAYSDCVE VAPVSCSPEP PDPSELYMTK SSRVKHLGLL
YISSLLVLVG YSILYGLTSK EARWLGALTS VAVVILDWNL GLCSFRFELL KSRMIVLFVA
GTSRAFLVSF GVHYWYLGHC ISYAFVASVL LSAAVSSWLS ISNPSVARID ALRSTVIKLR
EGFRRKGQNS SSNSSEGCGS SVKRSSGSVE AGQNGNAMDS MYRSNSQSDG VNWSSIPFDR
SNSCQEGRSS DKNIDSARAS LAHRSNSCLS AVQDSETAVV SVDRHGDPIT SLVCSSSGLE
SHGCEPSGSA TTSGNQQLLD LNLAAIFQDR LNDPRISSML KKNGGLGDVE LANLLQDKGL
DPNFSYMLKD KVMDPRILAL LQRSSLDADR EHQDDVDVTA TDSDRLDTTI ANQISLSEEL
RRSGLEKWLN ISRLIFHHLA GSPIRAFIVF TVMFIIETAT VAIYRPETIK VINATHEQFE
FGFSILLLSP VVCSIMAFIW SLRAEEMLMT SKPQKYGFIA WLLSTCVGLF LSFLSKSSVI
LGLSLTVPLM VACLSFAVPI WIRNGYSFWI PGREFANREN VSQAPGEKER ALFVITIAVF
TASIIGLGAI VSAKPLDALG YKGWDADKNS SYSPYATSMY LGWALSSTIA VITTGLIPIV
AWFATYRFSP SSAICVGLFA TVLVSFCGAS YWGVVNSRED GVPLKADFLA ALLPLLCIPA
FFSLFTGLYK WKDDDWKISR GVYLFVGMGM LLLFGAVAAV IVTIRPWTVG VACLVAILFL
VFVIGVIHYW TSNNFYLTRT QMLLVCSIAF LLALAAFLMG LFHGKPFVGA SIGYFSFIFL
LTGRALTVLL SPPIVVYSPR VLPVYVYDAH ADSAKNVSYA FLILYGIALA TEVWGVIASL
IMNPPFVGAG VSATTLVIAF SFAVSRPCLT LKMMEDAVHF LSKDTVVQAM SRSANKTRNA
ISGTYSAPQR SASSAALLVG DPALTLDRAG NFVLPRADVM KLRDRLRNEE IAAGSFLCGV
KDCLLICPQS LSNIDYRRNM CAHARILALE EAIDTEWVYM WDKFGGYLLL LLGLTAKAEQ
IQDEVRLRLF LDSIGLSDLS AKEIKKWMPE DRRQFELIQE SYIREKEMEE EALMQRREEE
GKGRERRRAL LEREERKWKE LEISLLSSIP NTGSRDAAAM AAAVRAVGGD SALEDSFARD
RVSSIANHIR KAQLARRAEQ TGIPGTICIL DDEPRSTGRH CGELDLCLCQ SQKVTLSIAV
MVQPVSGPVC LFGSEFQKVC WEILVAGSEQ GMEAGQVGLR LVTKGERMTT VAKEWNIGAS
SIADGRWHLV TVTLDADLGE ATSFIDGVYD GYQNGLPLPT DNGIWEPGTD IWVGARPPMD
LDAFGRSDSE GSDSKMQIMD AFLWGRCLSE DEVTVLHTAM SPAEYGFFDL APGDAWHGSY
SARVDDWESE EAYELYDQGD VEWDGQYSSG RKRPVHDAVA IDLDSFARRP RKPRFETRDE
VNQRMLSVER AVRDALIAKG ERNFTDQEFP PEDRSLFVDP MNPPLKLQVV SEWMRPSDIA
KDISISCQPC LFSGSVNSSD VCQGRLGDCW FLSAVAVLTE MSRISEVIIT PEYNDEGIYT
VRFCIQGEWV AVVVDDWIPC ESPGKPAFAT SRKQNELWVS ILEKAYAKLH GSYEALEGGL
VQDALVDLTG GAGEEIDMRS PQAQLDLASG RLWSQLLHFK QEGFLLGAGS PSGSDAHISS
SGIVQGHAYS ILQVREVDGH KLIQIRNPWA NEVEWNGPWS DSSPEWTERM KHKLMHVPQS
KNGVFWMSWQ DFQIHFRSIY VCRVYPPEMR YSVHGQWRGY NAGGCQDYDS WHQNPQYRLR
VTGRDALYPV HVFITLTQGV GFSRKTNGFR NYQSSHDSSM FYIGMRILKT QGCRAAYNIY
MHESAGGTDY VNSREISCEL VLDPYPKGYT IVPTTIHPGE EAPFVLSVFS KASIRLEAV


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U2250b CLIA Bos taurus,Bovine,Calcium-activated neutral proteinase 3,Calpain L3,Calpain p94,Calpain-3,CANP 3,CAPN3,Muscle-specific calcium-activated neutral protease 3,NCL1,nCL-1,New calpain 1 96T
E2249Rb Calcium-activated neutral proteinase 2,Calpain M-type,Calpain-2 catalytic subunit,Calpain-2 large subunit,CANP 2,CAPN2,M-calpain,Millimolar-calpain,Oryctolagus cuniculus,Rabbit
E2249b ELISA kit Bos taurus,Bovine,Calcium-activated neutral proteinase 2,Calpain M-type,Calpain-2 catalytic subunit,Calpain-2 large subunit,CANP 2,CAPN2,M-calpain,Millimolar-calpain 96T
E2249b ELISA Bos taurus,Bovine,Calcium-activated neutral proteinase 2,Calpain M-type,Calpain-2 catalytic subunit,Calpain-2 large subunit,CANP 2,CAPN2,M-calpain,Millimolar-calpain 96T


 

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