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Protein

Ribosome-inactivating protein PD-L3/PD-L4

Gene
N/A
Organism
Phytolacca dioica (Bella sombra tree) (Phytolacca arborea)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Inhibits protein synthesis. Does not cleave supercoiled pBR322 dsDNA.2 Publications

Catalytic activityi

Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei175 – 1751Sequence analysis

GO - Molecular functioni

  • rRNA N-glycosylase activity Source: UniProtKB

GO - Biological processi

  • defense response Source: UniProtKB
  • negative regulation of translation Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protein synthesis inhibitor, Toxin

Keywords - Biological processi

Plant defense

Enzyme and pathway databases

BRENDAi3.2.2.22. 9766.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosome-inactivating protein PD-L3/PD-L41 Publication (EC:3.2.2.22)
Alternative name(s):
rRNA N-glycosidase PD-L3/PD-L41 Publication
OrganismiPhytolacca dioica (Bella sombra tree) (Phytolacca arborea)
Taxonomic identifieri29725 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeCaryophyllalesPhytolaccaceaePhytolacca

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi211 – 2111S → A: Reduces activity on DNA, rRNA and poly(A). Does not affect activity on ribosomes or inhibition of protein synthesis. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 261261Ribosome-inactivating protein PD-L3/PD-L4PRO_0000235848Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi10 – 101N-linked (GlcNAc...); in PD-L3Sequence analysis2 Publications
Disulfide bondi34 ↔ 258Sequence analysis
Disulfide bondi84 ↔ 105Sequence analysis

Keywords - PTMi

Disulfide bond, Glycoprotein

Expressioni

Developmental stagei

Detected in developing and mature leaves of adult plants. Levels of PD-L3 and PD-L4 are highest during the spring and summer, fall in autumn and are low during winter. Not detected in young (8-34 month old) plants.1 Publication

Structurei

Secondary structure

1
261
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi13 – 2715Combined sources
Beta strandi37 – 393Combined sources
Beta strandi45 – 473Combined sources
Beta strandi49 – 557Combined sources
Beta strandi61 – 677Combined sources
Turni68 – 703Combined sources
Beta strandi73 – 808Combined sources
Beta strandi83 – 897Combined sources
Helixi94 – 10411Combined sources
Beta strandi110 – 1134Combined sources
Helixi122 – 1298Combined sources
Helixi134 – 1363Combined sources
Helixi141 – 15111Combined sources
Helixi159 – 17820Combined sources
Helixi180 – 1889Combined sources
Turni189 – 1913Combined sources
Helixi198 – 21619Combined sources
Beta strandi221 – 2299Combined sources
Beta strandi235 – 2406Combined sources
Helixi241 – 2444Combined sources
Helixi245 – 2473Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2QESX-ray1.24A1-261[»]
2QETX-ray1.24A1-261[»]
2Z4UX-ray1.10A1-261[»]
2Z53X-ray1.29A1-261[»]
ProteinModelPortaliP84854.
SMRiP84854. Positions 1-261.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP84854.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di3.40.420.10. 1 hit.
4.10.470.10. 1 hit.
InterProiIPR001574. Ribosome_inactivat_prot.
IPR017988. Ribosome_inactivat_prot_CS.
IPR016138. Ribosome_inactivat_prot_sub1.
IPR016139. Ribosome_inactivat_prot_sub2.
IPR017989. Ribosome_inactivat_prot_subgr.
[Graphical view]
PfamiPF00161. RIP. 1 hit.
[Graphical view]
PRINTSiPR00396. SHIGARICIN.
SUPFAMiSSF56371. SSF56371. 1 hit.
PROSITEiPS00275. SHIGA_RICIN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P84854-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
VNTITFDVGN ATINKYATFM ESLRNEAKDP TLKCYGIPML PDSNLTPKYV
60 70 80 90 100
LVKLQDASSK TITLMLRRNN LYVMGYSDLY NGKCRYHIFN DISSTESTDV
110 120 130 140 150
ENTLCPNSNS REKKAINYNS QYSTLQNKAG VSSRSQVQLG IQILNSDIGK
160 170 180 190 200
ISGVSTFTDK TEAEFLLVAI QMVSEAARFK YIENQVKTNF NRAFNPNPKV
210 220 230 240 250
LSLEENWGKI SLAIHNAKNG ALTSPLELKN ADDTKWIVLR VDEIKPDMGL
260
LNYVSGTCQT T
Length:261
Mass (Da):29,190
Last modified:May 29, 2007 - v2
Checksum:iD497355FC3B7C463
GO

Mass spectrometryi

Molecular mass is 30356±1 Da from positions 1 - 261. Determined by ESI. PD-L3.1 Publication
Molecular mass is 29185±1 Da from positions 1 - 261. Determined by ESI. PD-L4.1 Publication
Molecular mass is 30357.7 Da from positions 1 - 261. Determined by ESI. PD-L3.2 Publications

Cross-referencesi

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2QESX-ray1.24A1-261[»]
2QETX-ray1.24A1-261[»]
2Z4UX-ray1.10A1-261[»]
2Z53X-ray1.29A1-261[»]
ProteinModelPortaliP84854.
SMRiP84854. Positions 1-261.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.2.2.22. 9766.

Miscellaneous databases

EvolutionaryTraceiP84854.

Family and domain databases

Gene3Di3.40.420.10. 1 hit.
4.10.470.10. 1 hit.
InterProiIPR001574. Ribosome_inactivat_prot.
IPR017988. Ribosome_inactivat_prot_CS.
IPR016138. Ribosome_inactivat_prot_sub1.
IPR016139. Ribosome_inactivat_prot_sub2.
IPR017989. Ribosome_inactivat_prot_subgr.
[Graphical view]
PfamiPF00161. RIP. 1 hit.
[Graphical view]
PRINTSiPR00396. SHIGARICIN.
SUPFAMiSSF56371. SSF56371. 1 hit.
PROSITEiPS00275. SHIGA_RICIN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Invariant Ser211 is involved in the catalysis of PD-L4, type I RIP from Phytolacca dioica leaves."
    Chambery A., Pisante M., Di Maro A., Di Zazzo E., Ruvo M., Costantini S., Colonna G., Parente A.
    Proteins 67:209-218(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE, MUTAGENESIS OF SER-211.
    Tissue: Leaf1 Publication.
  2. "Structural characterization and comparative modeling of PD-Ls 1-3, type 1 ribosome-inactivating proteins from summer leaves of Phytolacca dioica L."
    Di Maro A., Chambery A., Carafa V., Costantini S., Colonna G., Parente A.
    Biochimie 91:352-363(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE, GLYCOSYLATION AT ASN-10, MASS SPECTROMETRY.
    Tissue: Leaf.
  3. "Isolation and characterization of four type-1 ribosome-inactivating proteins, with polynucleotide:adenosine glycosidase activity, from leaves of Phytolacca dioica L."
    Di Maro A., Valbonesi P., Bolognesi A., Stirpe F., De Luca P., Siniscalco Gigliano G., Gaudio L., Delli-Bovi P., Ferranti P., Malorni A., Parente A.
    Planta 208:125-131(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-45, GLYCOSYLATION AT ASN-10, FUNCTION, CATALYTIC ACTIVITY, MASS SPECTROMETRY.
    Tissue: Leaf1 Publication.
  4. "Nicking activity on pBR322 DNA of ribosome inactivating proteins from Phytolacca dioica L. leaves."
    Aceto S., Di Maro A., Conforto B., Siniscalco Gigliano G., Parente A., Delli-Bovi P., Gaudio L.
    Biol. Chem. 386:307-317(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
    Tissue: Leaf1 Publication.
  5. "Type 1 ribosome-inactivating proteins from Phytolacca dioica L. leaves: differential seasonal and age expression, and cellular localization."
    Parente A., Conforto B., Di Maro A., Chambery A., De Luca P., Bolognesi A., Iriti M., Faoro F.
    Planta 228:963-975(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE.
  6. "Atomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves."
    Ruggiero A., Chambery A., Di Maro A., Parente A., Berisio R.
    Proteins 71:8-15(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.10 ANGSTROMS) IN COMPLEX WITH ADENINE, MUTAGENESIS OF SER-211.

Entry informationi

Entry nameiRIPL2_PHYDI
AccessioniPrimary (citable) accession number: P84854
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: May 29, 2007
Last modified: December 9, 2015
This is version 41 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

2 forms exist, PD-L3 and PD-L4, that differ in their post-translational modifications. PD-L4 is not glycosylated.

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.