RIPL1_PHYDI
ID RIPL1_PHYDI Reviewed; 261 AA.
AC P84853;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 10-FEB-2009, sequence version 2.
DT 03-AUG-2022, entry version 58.
DE RecName: Full=Ribosome-inactivating protein PD-L1/PD-L2 {ECO:0000303|PubMed:10213004, ECO:0000303|PubMed:19452522, ECO:0000303|PubMed:20174685};
DE EC=3.2.2.22 {ECO:0000269|PubMed:10213004, ECO:0000269|PubMed:20174685};
DE AltName: Full=rRNA N-glycosidase PD-L1/PD-L2 {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]
RP PROTEIN SEQUENCE, GLYCOSYLATION AT ASN-10; ASN-43 AND ASN-255, AND MASS
RP 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 [2] {ECO:0000305}
RP PROTEIN SEQUENCE OF 1-45, GLYCOSYLATION AT ASN-43, 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 [3] {ECO:0007744|PDB:3LE7}
RP PROTEIN SEQUENCE OF 1-10, X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF PD-L1
RP IN COMPLEX WITH ADENINE, FUNCTION, CATALYTIC ACTIVITY, TISSUE SPECIFICITY,
RP PTM, GLYCOSYLATION AT ASN-10, DISULFIDE BONDS, AND CIRCULAR DICHROISM
RP ANALYSIS.
RX PubMed=20174685; DOI=10.1039/b919801f;
RA Severino V., Chambery A., Di Maro A., Marasco D., Ruggiero A., Berisio R.,
RA Giansanti F., Ippoliti R., Parente A.;
RT "The role of the glycan moiety on the structure-function relationships of
RT PD-L1, type 1 ribosome-inactivating protein from P. dioica leaves.";
RL Mol. Biosyst. 6:570-579(2010).
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] {ECO:0007744|PDB:3H5K}
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF PD-L1, FUNCTION, TISSUE
RP SPECIFICITY, PTM, GLYCOSYLATION AT ASN-10, AND DISULFIDE BONDS.
RX PubMed=19452522; DOI=10.1002/bip.21260;
RA Ruggiero A., Di Maro A., Severino V., Chambery A., Berisio R.;
RT "Crystal structure of PD-L1, a ribosome inactivating protein from
RT Phytolacca dioica L. leaves with the property to induce DNA cleavage.";
RL Biopolymers 91:1135-1142(2009).
CC -!- FUNCTION: Inhibits protein synthesis (PubMed:10213004,
CC PubMed:20174685). Has adenine polynucleotide glycosidase activity on
CC herring sperm (hs)DNA and poly(A) substrates (PubMed:20174685). Cleaves
CC supercoiled pBR322 dsDNA (PubMed:15899692, PubMed:19452522).
CC {ECO:0000269|PubMed:10213004, ECO:0000269|PubMed:15899692,
CC ECO:0000269|PubMed:19452522, ECO:0000269|PubMed:20174685}.
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, ECO:0000269|PubMed:20174685};
CC -!- TISSUE SPECIFICITY: Expressed in leaves (at protein level).
CC {ECO:0000269|PubMed:19452522, ECO:0000269|PubMed:20174685}.
CC -!- DEVELOPMENTAL STAGE: Detected in developing and mature leaves of adult
CC plants. Levels of PD-L1 are highest during the winter, levels of PD-L2
CC remain constant throughout the year. Not detected in young (8-34 month
CC old) plants. {ECO:0000269|PubMed:18704492}.
CC -!- PTM: N-glycosylated (PubMed:19452522, PubMed:20174685). Loss of
CC glycosylation does not affect DNA-cleaving ability (PubMed:19452522).
CC Loss of glycosylation does not affect protein synthesis inhibition, but
CC increases adenine polynucleotide glycosidase activity likely as a
CC consequence of the increased accessibility of substrates to the active
CC site pocket in the absence of glycosylation (PubMed:20174685).
CC {ECO:0000269|PubMed:19452522, ECO:0000269|PubMed:20174685}.
CC -!- MASS SPECTROMETRY: Mass=32715; Mass_error=1; Method=Electrospray;
CC Note=PD-L1.; Evidence={ECO:0000269|PubMed:10213004};
CC -!- MASS SPECTROMETRY: Mass=31542; Mass_error=1; Method=Electrospray;
CC Note=PD-L2.; Evidence={ECO:0000269|PubMed:10213004};
CC -!- MASS SPECTROMETRY: Mass=31560.50; Method=Electrospray; Note=PD-L2.;
CC Evidence={ECO:0000269|PubMed:19014994};
CC -!- MISCELLANEOUS: 2 forms exist, PD-L1 and PD-L2, that differ in their
CC post-translational modifications.
CC -!- SIMILARITY: Belongs to the ribosome-inactivating protein family. Type 1
CC RIP subfamily. {ECO:0000255}.
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DR PDB; 3H5K; X-ray; 1.45 A; A/B=1-261.
DR PDB; 3LE7; X-ray; 1.65 A; A/B=1-261.
DR PDBsum; 3H5K; -.
DR PDBsum; 3LE7; -.
DR AlphaFoldDB; P84853; -.
DR SMR; P84853; -.
DR iPTMnet; P84853; -.
DR BRENDA; 3.2.2.22; 9766.
DR EvolutionaryTrace; P84853; -.
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-L1/PD-L2"
FT /id="PRO_0000235847"
FT ACT_SITE 72
FT /evidence="ECO:0000250|UniProtKB:P84531"
FT ACT_SITE 122
FT /evidence="ECO:0000250|UniProtKB:P84531"
FT ACT_SITE 175
FT /evidence="ECO:0000250|UniProtKB:P84531"
FT ACT_SITE 178
FT /evidence="ECO:0000250|UniProtKB:P84531"
FT BINDING 73
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:20174685,
FT ECO:0007744|PDB:3LE7"
FT BINDING 120
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:20174685,
FT ECO:0007744|PDB:3LE7"
FT BINDING 178
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:20174685,
FT ECO:0007744|PDB:3LE7"
FT CARBOHYD 10
FT /note="N-linked (GlcNAc...) asparagine; in PD-L1 and PD-L2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498,
FT ECO:0000269|PubMed:19014994, ECO:0000269|PubMed:19452522,
FT ECO:0000269|PubMed:20174685, ECO:0007744|PDB:3H5K,
FT ECO:0007744|PDB:3LE7"
FT CARBOHYD 43
FT /note="N-linked (GlcNAc...) asparagine; in PD-L1 and PD-L2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498,
FT ECO:0000269|PubMed:10213004, ECO:0000269|PubMed:19014994"
FT CARBOHYD 255
FT /note="N-linked (GlcNAc...) asparagine; in PD-L1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498,
FT ECO:0000269|PubMed:19014994"
FT DISULFID 34..258
FT /evidence="ECO:0000269|PubMed:19452522,
FT ECO:0000269|PubMed:20174685, ECO:0007744|PDB:3H5K,
FT ECO:0007744|PDB:3LE7"
FT DISULFID 84..105
FT /evidence="ECO:0000269|PubMed:19452522,
FT ECO:0000269|PubMed:20174685, ECO:0007744|PDB:3H5K,
FT ECO:0007744|PDB:3LE7"
FT CONFLICT 31
FT /note="S -> Q (in Ref. 2; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 3..10
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 13..27
FT /evidence="ECO:0007829|PDB:3H5K"
FT STRAND 37..39
FT /evidence="ECO:0007829|PDB:3H5K"
FT STRAND 49..55
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 57..59
FT /evidence="ECO:0007829|PDB:3H5K"
FT STRAND 61..67
FT /evidence="ECO:0007829|PDB:3H5K"
FT TURN 68..70
FT /evidence="ECO:0007829|PDB:3H5K"
FT STRAND 73..80
FT /evidence="ECO:0007829|PDB:3H5K"
FT STRAND 83..89
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 95..104
FT /evidence="ECO:0007829|PDB:3H5K"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:3H5K"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:3H5K"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 122..128
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 134..136
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 141..151
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 159..172
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 174..178
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 180..188
FT /evidence="ECO:0007829|PDB:3H5K"
FT TURN 189..191
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 198..215
FT /evidence="ECO:0007829|PDB:3H5K"
FT STRAND 221..229
FT /evidence="ECO:0007829|PDB:3H5K"
FT STRAND 235..240
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 241..244
FT /evidence="ECO:0007829|PDB:3H5K"
FT HELIX 245..247
FT /evidence="ECO:0007829|PDB:3H5K"
SQ SEQUENCE 261 AA; 29222 MW; B4C78B6026FC7288 CRC64;
INTITYDAGN TTINKYATFM ESLRNEAKDP SLQCYGIPML PNNSSTIKYL LVKLQGASQK
TITLMLRRNN LYVMGYSDPF NGNCRYHIFN DITGTERTNV ENTLCSSSSS RDAKPINYNS
LYSTLEKKAE VNSRSQVQLG IQILSSDIGK ISGQSSFTDK TEAKFLLVAI QMVSEAARFK
YIENQVKTNF NRDFSPNDKI LDLEENWGKI STAIHDATNG ALPKPLELKN ADGTKWIVLR
VDEIKPDMGL LNYVNGTCQT T
