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Protein

Calpain-type cysteine protease ADL1

Gene

ADL1

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.3 Publications

Catalytic activityi

Broad endopeptidase specificity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei1772 – 17721By similarity
Active sitei1930 – 19301By similarity
Active sitei1950 – 19501By similarity

GO - Molecular functioni

GO - Biological processi

  • embryo development ending in seed dormancy Source: UniProtKB
  • epidermal cell fate specification Source: UniProtKB
  • proteolysis Source: GO_Central
  • regulation of adaxial/abaxial pattern formation Source: UniProtKB
  • regulation of cell growth Source: UniProtKB
  • regulation of cell proliferation Source: UniProtKB
  • regulation of endosperm development Source: UniProtKB
  • regulation of leaf development Source: UniProtKB
  • regulation of meristem structural organization Source: UniProtKB
  • self proteolysis Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Hydrolase, Protease, Thiol protease

Protein family/group databases

MEROPSiC02.019.

Names & Taxonomyi

Protein namesi
Recommended name:
Calpain-type cysteine protease ADL1 (EC:3.4.22.-)
Alternative name(s):
Phytocalpain ADL1
Protein ADAXIALIZED LEAF1
Protein DEFECTIVE KERNEL 1
Short name:
OsDEK1
Protein SHOOTLESS 3
Gene namesi
Name:ADL1
Synonyms:DEK1, ODM63, SHL3
Ordered Locus Names:Os02g0709400, LOC_Os02g47970
ORF Names:OJ1311_H06.4
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryza
Proteomesi
  • UP000059680 Componenti: Chromosome 2

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini34 – 7037ExtracellularSequence analysisAdd
BLAST
Transmembranei71 – 9121Helical; Name=1Sequence analysisAdd
BLAST
Topological domaini92 – 954CytoplasmicSequence analysis
Transmembranei96 – 11621Helical; Name=2Sequence analysisAdd
BLAST
Topological domaini117 – 12711ExtracellularSequence analysisAdd
BLAST
Transmembranei128 – 14821Helical; Name=3Sequence analysisAdd
BLAST
Topological domaini149 – 16416CytoplasmicSequence analysisAdd
BLAST
Transmembranei165 – 18521Helical; Name=4Sequence analysisAdd
BLAST
Topological domaini186 – 23651ExtracellularSequence analysisAdd
BLAST
Transmembranei237 – 25721Helical; Name=5Sequence analysisAdd
BLAST
Topological domaini258 – 2647CytoplasmicSequence analysis
Transmembranei265 – 28521Helical; Name=6Sequence analysisAdd
BLAST
Topological domaini286 – 2949ExtracellularSequence analysis
Transmembranei295 – 31521Helical; Name=7Sequence analysisAdd
BLAST
Topological domaini316 – 3205CytoplasmicSequence analysis
Transmembranei321 – 34121Helical; Name=8Sequence analysisAdd
BLAST
Topological domaini342 – 626285ExtracellularSequence analysisAdd
BLAST
Transmembranei627 – 64721Helical; Name=9Sequence analysisAdd
BLAST
Topological domaini648 – 66316CytoplasmicSequence analysisAdd
BLAST
Transmembranei664 – 68421Helical; Name=10Sequence analysisAdd
BLAST
Topological domaini685 – 69713ExtracellularSequence analysisAdd
BLAST
Transmembranei698 – 71821Helical; Name=11Sequence analysisAdd
BLAST
Topological domaini719 – 7224CytoplasmicSequence analysis
Transmembranei723 – 74321Helical; Name=12Sequence analysisAdd
BLAST
Topological domaini744 – 77330ExtracellularSequence analysisAdd
BLAST
Transmembranei774 – 79421Helical; Name=13Sequence analysisAdd
BLAST
Topological domaini795 – 82531CytoplasmicSequence analysisAdd
BLAST
Transmembranei826 – 84621Helical; Name=14Sequence analysisAdd
BLAST
Topological domaini847 – 85610ExtracellularSequence analysis
Transmembranei857 – 87721Helical; Name=15Sequence analysisAdd
BLAST
Topological domaini878 – 89013CytoplasmicSequence analysisAdd
BLAST
Transmembranei891 – 91121Helical; Name=16Sequence analysisAdd
BLAST
Topological domaini912 – 92413ExtracellularSequence analysisAdd
BLAST
Transmembranei925 – 94521Helical; Name=17Sequence analysisAdd
BLAST
Topological domaini946 – 9494CytoplasmicSequence analysis
Transmembranei950 – 97021Helical; Name=18Sequence analysisAdd
BLAST
Topological domaini971 – 98414ExtracellularSequence analysisAdd
BLAST
Transmembranei985 – 100521Helical; Name=19Sequence analysisAdd
BLAST
Topological domaini1006 – 101914CytoplasmicSequence analysisAdd
BLAST
Transmembranei1020 – 104021Helical; Name=20Sequence analysisAdd
BLAST
Topological domaini1041 – 106323ExtracellularSequence analysisAdd
BLAST
Transmembranei1064 – 108421Helical; Name=21Sequence analysisAdd
BLAST
Topological domaini1085 – 21621078CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cytoplasm, Endoplasmic reticulum, Endosome, Membrane

Pathology & Biotechi

Disruption phenotypei

Abnormal embryos arrested at the globular stage with an abnormal aleurone layer on the ventral side.3 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi1776 – 17761S → N in adl1-s1 and shl3-1; deletion of the apical region including the shoot apical meristem (SAM), coleoptile, and scutellum in embryos, and no clear root organization. 1 Publication
Mutagenesisi1777 – 17771A → V in adl1-2; abaxially rolled leaves covered with bulliform-like cells, which are normally distributed only on the adaxial surface; this adaxialization concerns both epidermal and mesophyll tissues. Larger L1 cells in shoot apical meristems (SAM).
Mutagenesisi1841 – 18411W → R in adl1-g1 and odm-63; abnormal embryos arrested at the globular stage with an abnormal aleurone layer on the ventral side. 1 Publication
Mutagenesisi2110 – 21101G → R in adl1-1; abaxially rolled leaves covered with bulliform-like cells, which are normally distributed only on the adaxial surface; this adaxialization concerns both epidermal and mesophyll tissues. Larger L1 cells in shoot apical meristems (SAM).

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3333Sequence analysisAdd
BLAST
Chaini34 – 21622129Calpain-type cysteine protease ADL1PRO_0000423441Add
BLAST
Propeptidei34 – ?By similarityPRO_0000423442

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1372 – 13721PhosphoserineBy similarity
Modified residuei1377 – 13771PhosphoserineBy similarity
Modified residuei1668 – 16681PhosphoserineBy similarity

Post-translational modificationi

Autocatalytic proteolytic cleavage leading to the production of mainly cytoplasmic localized subproducts of about 85 and 120 kDa.By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ6ZFZ4.

PTM databases

iPTMnetiQ6ZFZ4.

Expressioni

Tissue specificityi

Ubiquitously expressed with higher levels in embryos, vasculatures, leaf primordia, leaf margins, and shoot apical meristem (SAM).1 Publication

Gene expression databases

GenevisibleiQ6ZFZ4. OS.

Interactioni

Protein-protein interaction databases

STRINGi39947.LOC_Os02g47970.1.

Structurei

3D structure databases

ProteinModelPortaliQ6ZFZ4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1418 – 1611194Calpain catalytic 1PROSITE-ProRule annotationAdd
BLAST
Domaini1706 – 2008303Calpain catalytic 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi1249 – 12557Poly-Leu

Domaini

The transmembrane regions are not required for calpain activity but may play regulatory roles.By similarity

Sequence similaritiesi

Belongs to the peptidase C2 family.Curated
Contains 2 calpain catalytic domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG0045. Eukaryota.
ENOG410XP0B. LUCA.
HOGENOMiHOG000030613.
InParanoidiQ6ZFZ4.

Family and domain databases

Gene3Di2.60.120.200. 1 hit.
InterProiIPR022684. Calpain_cysteine_protease.
IPR022682. Calpain_domain_III.
IPR022683. Calpain_III.
IPR013320. ConA-like_dom.
IPR000169. Pept_cys_AS.
IPR001300. Peptidase_C2_calpain_cat.
[Graphical view]
PfamiPF01067. Calpain_III. 1 hit.
PF00648. Peptidase_C2. 1 hit.
[Graphical view]
PRINTSiPR00704. CALPAIN.
SMARTiSM00720. calpain_III. 1 hit.
SM00230. CysPc. 1 hit.
[Graphical view]
SUPFAMiSSF49758. SSF49758. 1 hit.
SSF49899. SSF49899. 1 hit.
PROSITEiPS50203. CALPAIN_CAT. 1 hit.
PS00139. THIOL_PROTEASE_CYS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q6ZFZ4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEEEEHRGVV LVCSICGFLF AVLGPLSFWI LWAVNWRPWR LYSWIYARKW
60 70 80 90 100
PAYVQGPQLS TLCSFFTLFA WLVVVSPITV LLVWGGILIA LLERNIIGLA
110 120 130 140 150
VIMVGVALLL SFYSIMLWWR TQWQSSKAVA YLLLLAVGLL CAYEFCAVYV
160 170 180 190 200
TTGASASELN SPSGFFFGVS AISLAINMLF ISKILFNGSG FDVDEYVRRL
210 220 230 240 250
YKFAYSDCVE VAPVSCSPDP PDPSELYMTK SSRVLHLGLL YLCSLMVLVV
260 270 280 290 300
YSILYGLTSK EARWLGALTS VAVVILDWNL GLCSFRFELL KSRMIALFVA
310 320 330 340 350
GTSRVFLICF GVHYWYLGHC ISYAFVASVL LAAAVSCWLS ISNPSVARID
360 370 380 390 400
ALRSTVIKLR EGFRRKGQTS SSNSSDGCGS SVKRSSGSVE AGPHGNATDS
410 420 430 440 450
MYRSNSQSDC VNWNNVPFDR SNSCQEGQSS DKNIDSGRAS LAHRSNSCLS
460 470 480 490 500
AVAVQDPETA VVSADRHGDP TASLVVCSSS GLESQGCESS GSATASGNQQ
510 520 530 540 550
LLDLNLAAIF QDRLNDPRIT SMLKRNGGLG DVELANLLQD KGLDPNFSYM
560 570 580 590 600
MKDKVMDPRI LALLQRSSLD ADREHQDDVD VTGTDSDRLD TTIANQISLS
610 620 630 640 650
EELRRSGLEN WLNLSRLMFH QVAGSPIRAF VVFTLIFIIE TVTVAVHRPK
660 670 680 690 700
PIKVINATHE QFEFGFSILL LSPVVCSIMA FIWSLCAEEM TMTSKPRKYG
710 720 730 740 750
FIAWLLSTCV GLLLSFLSKS SVILGLSLTV PLMVACLSFA IPIWMRNGYR
760 770 780 790 800
FWIPGGELDS RENIRQAPGK KERALFAISI TVFTASVIGL GAIVSAKPLD
810 820 830 840 850
ALGYKGWDAD KKSFYSPYAT SMYLGWALSS TIAVLATGVI PIVAWFATYR
860 870 880 890 900
FSPSSAICVG LFATVLVSFC GVSYWGVVNS RQDGVPLKAD FLAALLPLLC
910 920 930 940 950
IPAVFSLFTG MYKWKDDDWK ISRGVYLFVG MGVLLLLGAI SAVIVTIRPW
960 970 980 990 1000
TVGVACLLVI LFLVFAIGVI HYWTSNNFYL TRTQMLLVCS LAFLLALAAF
1010 1020 1030 1040 1050
LMGLFQEKPF VGASIGYFSF LFLLTGRALT VLLSPPIVVY SPRVLPVYVY
1060 1070 1080 1090 1100
DAHADSAKNV SYAFLILYGI ALATEVWGVI ASLILNPPFI GAAISAITLV
1110 1120 1130 1140 1150
IAFSFAVSRP CLTLKMLEDA VHFLSKDTVV QAMSRSANKT RNAISGTYSA
1160 1170 1180 1190 1200
PQRSASSAAL LVGDPAITLD RAGNFVLPRA DVMKLRDRLR NEEITAGSFF
1210 1220 1230 1240 1250
CGVKNCLMIG SPVDVDYRRN MCAHARILAL EEAIDTEWVY MWDKFGGYLL
1260 1270 1280 1290 1300
LLLGLTAKAE QIQDEVRLRL FLDSIGLSDL SAKEIKKWMP EDRRHFELIQ
1310 1320 1330 1340 1350
ESYIREKEME EEVLMQRREE EGKGRERRKA LLEREERKWK ELEISLLSSI
1360 1370 1380 1390 1400
PNAGSRDAAA MAAAVRAVGG DSALEDSFAR DRVSSIARHI RKAQLARRAE
1410 1420 1430 1440 1450
QTGIPDTVCI LDDEPRSTGR HCGEIDLCLC ESKKVSFSIA VMVQPVSGPV
1460 1470 1480 1490 1500
CLFGTEFQKK VCWEILVAGS EQGMEAGQVG LRLVTKGERM TTVAKEWNIG
1510 1520 1530 1540 1550
ASSIADGRWH LVTVTIDADL GEATSFIDGV YDGYQNALPL PRNNGIWEPG
1560 1570 1580 1590 1600
TDIWVGARPP TDLDAFGRSD SEGSDSKMQI MDAFLWGRCL TEDEVAMLHT
1610 1620 1630 1640 1650
AICSAEYGLF DLAAEDAWHG SYSARVDDWE SEEANFELYD QEDVEWDGQY
1660 1670 1680 1690 1700
SSGRKRHARD SVAIDIDSFA RRPRKPRFET REEVNQRMLS VERAVREALI
1710 1720 1730 1740 1750
AKGERNFTDQ EFPPDDRSLF VDPMNPSLKL QVVSEWMRPS DIAKEVSISS
1760 1770 1780 1790 1800
QPCLFSGSVN SSDVCQGRLG DCWFLSAVAV LTEMARISEV IITPEYNEEG
1810 1820 1830 1840 1850
IYTVRFCIQG EWVAVVVDDW IPCESPGKPA FATSRKQNEL WVSILEKAYA
1860 1870 1880 1890 1900
KLHGSYEALE GGLVQDALVD LTGGAGEEID MRSPQAQIDL ASGRLWSQLL
1910 1920 1930 1940 1950
HFKQEGFLLG AGSPSGSDAH ISSSGIVQGH AYSILQVREV DGHKLVQIRN
1960 1970 1980 1990 2000
PWANEVEWNG PWSDSSQEWT ERMKHKLKHV PQSKNGVFWM SWQDFQIHFR
2010 2020 2030 2040 2050
SIYVCRVYPP EMRYSVHGQW RGYSAGGCQD YDSWHQNPQY RLRVTGRDAL
2060 2070 2080 2090 2100
YPVHVFITLT QGVGFSRKTN GFRNYQSSHD SSMFYIGMRI LKTRGCRAAY
2110 2120 2130 2140 2150
NIYMHESVGG TDYVNSREIS CELVLEPYPK GYTIVPTTIH PGEEAPFVLS
2160
VFTKAPIKLE AV
Length:2,162
Mass (Da):239,859
Last modified:July 5, 2004 - v1
Checksum:i9FF44A8AE2B23F0B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti42 – 421Y → F in AAL38190 (PubMed:11929961).Curated
Sequence conflicti713 – 7131L → F in AAL38190 (PubMed:11929961).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB477099 mRNA. Translation: BAI44850.1.
AY062272 mRNA. Translation: AAL38190.1.
AP004161 Genomic DNA. Translation: BAD07761.1.
AP008208 Genomic DNA. Translation: BAF09804.1.
AP014958 Genomic DNA. No translation available.
RefSeqiXP_015625425.1. XM_015769939.1.
XP_015625426.1. XM_015769940.1.
UniGeneiOs.11709.

Genome annotation databases

GeneIDi4330484.
KEGGiosa:4330484.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB477099 mRNA. Translation: BAI44850.1.
AY062272 mRNA. Translation: AAL38190.1.
AP004161 Genomic DNA. Translation: BAD07761.1.
AP008208 Genomic DNA. Translation: BAF09804.1.
AP014958 Genomic DNA. No translation available.
RefSeqiXP_015625425.1. XM_015769939.1.
XP_015625426.1. XM_015769940.1.
UniGeneiOs.11709.

3D structure databases

ProteinModelPortaliQ6ZFZ4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Os02g47970.1.

Protein family/group databases

MEROPSiC02.019.

PTM databases

iPTMnetiQ6ZFZ4.

Proteomic databases

PaxDbiQ6ZFZ4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi4330484.
KEGGiosa:4330484.

Phylogenomic databases

eggNOGiKOG0045. Eukaryota.
ENOG410XP0B. LUCA.
HOGENOMiHOG000030613.
InParanoidiQ6ZFZ4.

Gene expression databases

GenevisibleiQ6ZFZ4. OS.

Family and domain databases

Gene3Di2.60.120.200. 1 hit.
InterProiIPR022684. Calpain_cysteine_protease.
IPR022682. Calpain_domain_III.
IPR022683. Calpain_III.
IPR013320. ConA-like_dom.
IPR000169. Pept_cys_AS.
IPR001300. Peptidase_C2_calpain_cat.
[Graphical view]
PfamiPF01067. Calpain_III. 1 hit.
PF00648. Peptidase_C2. 1 hit.
[Graphical view]
PRINTSiPR00704. CALPAIN.
SMARTiSM00720. calpain_III. 1 hit.
SM00230. CysPc. 1 hit.
[Graphical view]
SUPFAMiSSF49758. SSF49758. 1 hit.
SSF49899. SSF49899. 1 hit.
PROSITEiPS50203. CALPAIN_CAT. 1 hit.
PS00139. THIOL_PROTEASE_CYS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The ADAXIALIZED LEAF1 gene functions in leaf and embryonic pattern formation in rice."
    Hibara K., Obara M., Hayashida E., Abe M., Ishimaru T., Satoh H., Itoh J., Nagato Y.
    Dev. Biol. 334:345-354(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY.
    Strain: cv. Taichung 65.
  2. "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."
    Lid S.E., Gruis D., Jung R., Lorentzen J.A., Ananiev E., Chamberlin M., Niu X., Meeley R., Nichols S., Olsen O.-A.
    Proc. Natl. Acad. Sci. U.S.A. 99:5460-5465(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  4. "The rice annotation project database (RAP-DB): 2008 update."
    The rice annotation project (RAP)
    Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  5. Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  6. "Phenotypic diversity of 188 rice embryo mutants."
    Hong S.K., Aoki T., Kitano H., Satoh H., Nagato Y.
    Dev. Genet. 16:298-310(1995)
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF TRP-1841.
  7. "Initiation of shoot apical meristem in rice: characterization of four SHOOTLESS genes."
    Satoh N., Hong S.-K., Nishimura A., Matsuoka M., Kitano H., Nagato Y.
    Development 126:3629-3636(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF SER-1776.
    Strain: cv. Taichung 65.

Entry informationi

Entry nameiDEK1_ORYSJ
AccessioniPrimary (citable) accession number: Q6ZFZ4
Secondary accession number(s): Q8RYA5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 18, 2013
Last sequence update: July 5, 2004
Last modified: June 8, 2016
This is version 92 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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.By similarity

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  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.