RIPL2_PHYDI
ID RIPL2_PHYDI Reviewed; 261 AA.
AC P84854;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 29-MAY-2007, sequence version 2.
DT 25-MAY-2022, entry version 56.
DE RecName: Full=Ribosome-inactivating protein PD-L3/PD-L4 {ECO:0000303|PubMed:10213004};
DE EC=3.2.2.22;
DE AltName: Full=rRNA N-glycosidase PD-L3/PD-L4 {ECO:0000303|PubMed:10213004};
OS Phytolacca dioica (Bella sombra tree) (Phytolacca arborea).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC Caryophyllales; Phytolaccaceae; Phytolacca.
OX NCBI_TaxID=29725;
RN [1] {ECO:0000305}
RP PROTEIN SEQUENCE, AND MUTAGENESIS OF SER-211.
RC TISSUE=Leaf {ECO:0000269|PubMed:17243169};
RX PubMed=17243169; DOI=10.1002/prot.21271;
RA Chambery A., Pisante M., Di Maro A., Di Zazzo E., Ruvo M., Costantini S.,
RA Colonna G., Parente A.;
RT "Invariant Ser211 is involved in the catalysis of PD-L4, type I RIP from
RT Phytolacca dioica leaves.";
RL Proteins 67:209-218(2007).
RN [2]
RP PROTEIN SEQUENCE, GLYCOSYLATION AT ASN-10, AND MASS SPECTROMETRY.
RC TISSUE=Leaf;
RX PubMed=19014994; DOI=10.1016/j.biochi.2008.10.008;
RA Di Maro A., Chambery A., Carafa V., Costantini S., Colonna G., Parente A.;
RT "Structural characterization and comparative modeling of PD-Ls 1-3, type 1
RT ribosome-inactivating proteins from summer leaves of Phytolacca dioica L.";
RL Biochimie 91:352-363(2009).
RN [3] {ECO:0000305}
RP PROTEIN SEQUENCE OF 1-45, GLYCOSYLATION AT ASN-10, FUNCTION, CATALYTIC
RP ACTIVITY, AND MASS SPECTROMETRY.
RC TISSUE=Leaf {ECO:0000269|PubMed:10213004};
RX PubMed=10213004; DOI=10.1007/s004250050542;
RA Di Maro A., Valbonesi P., Bolognesi A., Stirpe F., De Luca P.,
RA Siniscalco Gigliano G., Gaudio L., Delli-Bovi P., Ferranti P., Malorni A.,
RA Parente A.;
RT "Isolation and characterization of four type-1 ribosome-inactivating
RT proteins, with polynucleotide:adenosine glycosidase activity, from leaves
RT of Phytolacca dioica L.";
RL Planta 208:125-131(1999).
RN [4] {ECO:0000305}
RP FUNCTION.
RC TISSUE=Leaf {ECO:0000269|PubMed:15899692};
RX PubMed=15899692; DOI=10.1515/bc.2005.037;
RA Aceto S., Di Maro A., Conforto B., Siniscalco Gigliano G., Parente A.,
RA Delli-Bovi P., Gaudio L.;
RT "Nicking activity on pBR322 DNA of ribosome inactivating proteins from
RT Phytolacca dioica L. leaves.";
RL Biol. Chem. 386:307-317(2005).
RN [5] {ECO:0000305}
RP DEVELOPMENTAL STAGE.
RX PubMed=18704492; DOI=10.1007/s00425-008-0796-z;
RA Parente A., Conforto B., Di Maro A., Chambery A., De Luca P., Bolognesi A.,
RA Iriti M., Faoro F.;
RT "Type 1 ribosome-inactivating proteins from Phytolacca dioica L. leaves:
RT differential seasonal and age expression, and cellular localization.";
RL Planta 228:963-975(2008).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.10 ANGSTROMS) IN COMPLEX WITH ADENINE, AND
RP MUTAGENESIS OF SER-211.
RX PubMed=17963235; DOI=10.1002/prot.21712;
RA Ruggiero A., Chambery A., Di Maro A., Parente A., Berisio R.;
RT "Atomic resolution (1.1 A) structure of the ribosome-inactivating protein
RT PD-L4 from Phytolacca dioica L. leaves.";
RL Proteins 71:8-15(2008).
CC -!- FUNCTION: Inhibits protein synthesis. Does not cleave supercoiled
CC pBR322 dsDNA. {ECO:0000269|PubMed:10213004,
CC ECO:0000269|PubMed:15899692}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endohydrolysis of the N-glycosidic bond at one specific
CC adenosine on the 28S rRNA.; EC=3.2.2.22;
CC Evidence={ECO:0000269|PubMed:10213004};
CC -!- DEVELOPMENTAL STAGE: Detected in developing and mature leaves of adult
CC plants. Levels of PD-L3 and PD-L4 are highest during the spring and
CC summer, fall in autumn and are low during winter. Not detected in young
CC (8-34 month old) plants. {ECO:0000269|PubMed:18704492}.
CC -!- MASS SPECTROMETRY: Mass=30356; Mass_error=1; Method=Electrospray;
CC Note=PD-L3.; Evidence={ECO:0000269|PubMed:10213004};
CC -!- MASS SPECTROMETRY: Mass=29185; Mass_error=1; Method=Electrospray;
CC Note=PD-L4.; Evidence={ECO:0000269|PubMed:10213004};
CC -!- MASS SPECTROMETRY: Mass=30357.7; Method=Electrospray; Note=PD-L3.;
CC Evidence={ECO:0000269|PubMed:10213004, ECO:0000269|PubMed:19014994};
CC -!- MISCELLANEOUS: 2 forms exist, PD-L3 and PD-L4, that differ in their
CC post-translational modifications. PD-L4 is not glycosylated.
CC -!- SIMILARITY: Belongs to the ribosome-inactivating protein family. Type 1
CC RIP subfamily. {ECO:0000255}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR PDB; 2QES; X-ray; 1.24 A; A=1-261.
DR PDB; 2QET; X-ray; 1.24 A; A=1-261.
DR PDB; 2Z4U; X-ray; 1.10 A; A=1-261.
DR PDB; 2Z53; X-ray; 1.29 A; A=1-261.
DR PDBsum; 2QES; -.
DR PDBsum; 2QET; -.
DR PDBsum; 2Z4U; -.
DR PDBsum; 2Z53; -.
DR AlphaFoldDB; P84854; -.
DR SMR; P84854; -.
DR iPTMnet; P84854; -.
DR BRENDA; 3.2.2.22; 9766.
DR EvolutionaryTrace; P84854; -.
DR GO; GO:0030598; F:rRNA N-glycosylase activity; IDA:UniProtKB.
DR GO; GO:0090729; F:toxin activity; IEA:UniProtKB-KW.
DR GO; GO:0006952; P:defense response; IDA:UniProtKB.
DR GO; GO:0017148; P:negative regulation of translation; IDA:UniProtKB.
DR Gene3D; 3.40.420.10; -; 1.
DR Gene3D; 4.10.470.10; -; 1.
DR InterPro; IPR036041; Ribosome-inact_prot_sf.
DR InterPro; IPR017989; Ribosome_inactivat_1/2.
DR InterPro; IPR001574; Ribosome_inactivat_prot.
DR InterPro; IPR017988; Ribosome_inactivat_prot_CS.
DR InterPro; IPR016138; Ribosome_inactivat_prot_sub1.
DR InterPro; IPR016139; Ribosome_inactivat_prot_sub2.
DR PANTHER; PTHR33453; PTHR33453; 1.
DR Pfam; PF00161; RIP; 1.
DR PRINTS; PR00396; SHIGARICIN.
DR SUPFAM; SSF56371; SSF56371; 1.
DR PROSITE; PS00275; SHIGA_RICIN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Disulfide bond; Glycoprotein;
KW Hydrolase; Plant defense; Protein synthesis inhibitor; Toxin.
FT CHAIN 1..261
FT /note="Ribosome-inactivating protein PD-L3/PD-L4"
FT /id="PRO_0000235848"
FT ACT_SITE 175
FT /evidence="ECO:0000255"
FT CARBOHYD 10
FT /note="N-linked (GlcNAc...) asparagine; in PD-L3"
FT /evidence="ECO:0000255, ECO:0000269|PubMed:10213004,
FT ECO:0000269|PubMed:19014994"
FT DISULFID 34..258
FT /evidence="ECO:0000255"
FT DISULFID 84..105
FT /evidence="ECO:0000255"
FT MUTAGEN 211
FT /note="S->A: Reduces activity on DNA, rRNA and poly(A).
FT Does not affect activity on ribosomes or inhibition of
FT protein synthesis."
FT /evidence="ECO:0000269|PubMed:17243169,
FT ECO:0000269|PubMed:17963235"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:2Z4U"
FT HELIX 13..27
FT /evidence="ECO:0007829|PDB:2Z4U"
FT STRAND 37..39
FT /evidence="ECO:0007829|PDB:2Z4U"
FT STRAND 45..47
FT /evidence="ECO:0007829|PDB:2Z4U"
FT STRAND 49..55
FT /evidence="ECO:0007829|PDB:2Z4U"
FT STRAND 61..67
FT /evidence="ECO:0007829|PDB:2Z4U"
FT TURN 68..70
FT /evidence="ECO:0007829|PDB:2Z4U"
FT STRAND 73..80
FT /evidence="ECO:0007829|PDB:2Z4U"
FT STRAND 83..89
FT /evidence="ECO:0007829|PDB:2Z4U"
FT HELIX 94..104
FT /evidence="ECO:0007829|PDB:2Z4U"
FT STRAND 110..113
FT /evidence="ECO:0007829|PDB:2Z4U"
FT HELIX 122..129
FT /evidence="ECO:0007829|PDB:2Z4U"
FT HELIX 134..136
FT /evidence="ECO:0007829|PDB:2Z4U"
FT HELIX 141..151
FT /evidence="ECO:0007829|PDB:2Z4U"
FT HELIX 159..178
FT /evidence="ECO:0007829|PDB:2Z4U"
FT HELIX 180..188
FT /evidence="ECO:0007829|PDB:2Z4U"
FT TURN 189..191
FT /evidence="ECO:0007829|PDB:2Z4U"
FT HELIX 198..216
FT /evidence="ECO:0007829|PDB:2Z4U"
FT STRAND 221..229
FT /evidence="ECO:0007829|PDB:2Z4U"
FT STRAND 235..240
FT /evidence="ECO:0007829|PDB:2Z4U"
FT HELIX 241..244
FT /evidence="ECO:0007829|PDB:2Z4U"
FT HELIX 245..247
FT /evidence="ECO:0007829|PDB:2Z4U"
SQ SEQUENCE 261 AA; 29190 MW; D497355FC3B7C463 CRC64;
VNTITFDVGN ATINKYATFM ESLRNEAKDP TLKCYGIPML PDSNLTPKYV LVKLQDASSK
TITLMLRRNN LYVMGYSDLY NGKCRYHIFN DISSTESTDV ENTLCPNSNS REKKAINYNS
QYSTLQNKAG VSSRSQVQLG IQILNSDIGK ISGVSTFTDK TEAEFLLVAI QMVSEAARFK
YIENQVKTNF NRAFNPNPKV LSLEENWGKI SLAIHNAKNG ALTSPLELKN ADDTKWIVLR
VDEIKPDMGL LNYVSGTCQT T
