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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)DescriptionActionsGraphical viewLength
Active sitei175Sequence analysis1

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)DescriptionActionsGraphical viewLength
Mutagenesisi211S → A: Reduces activity on DNA, rRNA and poly(A). Does not affect activity on ribosomes or inhibition of protein synthesis. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002358481 – 261Ribosome-inactivating protein PD-L3/PD-L4Add BLAST261

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi10N-linked (GlcNAc...); in PD-L3Sequence analysis2 Publications1
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

1261
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Helixi13 – 27Combined sources15
Beta strandi37 – 39Combined sources3
Beta strandi45 – 47Combined sources3
Beta strandi49 – 55Combined sources7
Beta strandi61 – 67Combined sources7
Turni68 – 70Combined sources3
Beta strandi73 – 80Combined sources8
Beta strandi83 – 89Combined sources7
Helixi94 – 104Combined sources11
Beta strandi110 – 113Combined sources4
Helixi122 – 129Combined sources8
Helixi134 – 136Combined sources3
Helixi141 – 151Combined sources11
Helixi159 – 178Combined sources20
Helixi180 – 188Combined sources9
Turni189 – 191Combined sources3
Helixi198 – 216Combined sources19
Beta strandi221 – 229Combined sources9
Beta strandi235 – 240Combined sources6
Helixi241 – 244Combined sources4
Helixi245 – 247Combined sources3

3D structure databases

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

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: November 2, 2016
This is version 43 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.