Reviewed, UniProtKB/Swiss-Prot P84853 (RIPL1_PHYDI)

Names and origin

Protein names	Recommended name:     Ribosome-inactivating protein PD-L1/PD-L2     EC=3.2.2.22 Alternative name(s):     rRNA N-glycosidase PD-L1/PD-L2
Organism	Phytolacca dioica (Bella sombra tree) (Phytolacca arborea)
Taxonomic identifier	29725 [NCBI]
Taxonomic lineage	Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › Caryophyllales › Phytolaccaceae › Phytolacca

Protein attributes

Sequence length	261 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Inhibits protein synthesis. Cleaves supercoiled pBR322 dsDNA. Ref.2 Ref.3
Catalytic activity	Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA. Ref.2
Developmental stage	Detected in developing and mature leaves of adult plants. Levels of PD-L1 are highest during the winter, levels of PD-L2 remain constant throughout the year. Not detected in young (8-34 month old) plants. Ref.4
Miscellaneous	2 forms exist, PD-L1 and PD-L2, that differ in their post-translational modifications.
Sequence similarities	Belongs to the ribosome-inactivating protein family. Type 1 RIP subfamily.
Mass spectrometry	Molecular mass is 32715±1 Da from positions 1 - 261. Determined by ESI. PD-L1. Ref.2 Molecular mass is 31542±1 Da from positions 1 - 261. Determined by ESI. PD-L2. Ref.2 Molecular mass is 31560.50 Da from positions 1 - 261. Determined by ESI. PD-L2. Ref.1

Ontologies

Keywords
Biological process	Plant defense
Molecular function	Hydrolase Protein synthesis inhibitor Toxin
PTM	Disulfide bond Glycoprotein
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	defense response Ref.2 Inferred from direct assay. Source: UniProtKB negative regulation of translation Ref.2 Inferred from direct assay. Source: UniProtKB pathogenesis Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	rRNA N-glycosylase activity Ref.2 Inferred from direct assay. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 261	261	Ribosome-inactivating protein PD-L1/PD-L2		PRO_0000235847
Sites
	Active site	175	1	By similarity
Amino acid modifications
	Glycosylation	10	1	N-linked (GlcNAc...); in PD-L1 and PD-L2 Ref.1
	Glycosylation	42	1	N-linked (GlcNAc...); in PD-L1 and PD-L2 Ref.2 Ref.1
	Glycosylation	255	1	N-linked (GlcNAc...); in PD-L1 Ref.1
	Disulfide bond	34 ↔ 258		By similarity
	Disulfide bond	84 ↔ 105		By similarity
Experimental info
	Sequence conflict	31	1	S → Q AA sequence Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P84853-1 [UniParc]. Last modified February 10, 2009. Version 2. Checksum: B4C78B6026FC7288	FASTA	261	29,222
	10 20 30 40 50 60 INTITYDAGN TTINKYATFM ESLRNEAKDP SLQCYGIPML PNNSSTIKYL LVKLQGASQK 70 80 90 100 110 120 TITLMLRRNN LYVMGYSDPF NGNCRYHIFN DITGTERTNV ENTLCSSSSS RDAKPINYNS 130 140 150 160 170 180 LYSTLEKKAE VNSRSQVQLG IQILSSDIGK ISGQSSFTDK TEAKFLLVAI QMVSEAARFK 190 200 210 220 230 240 YIENQVKTNF NRDFSPNDKI LDLEENWGKI STAIHDATNG ALPKPLELKN ADGTKWIVLR 250 260 VDEIKPDMGL LNYVNGTCQT T

References

[1]	"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: 19014994] [Abstract] Cited for: PROTEIN SEQUENCE, GLYCOSYLATION AT ASN-10; ASN-42 AND ASN-255, MASS SPECTROMETRY. Tissue: Leaf.
[2]	"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: 10213004] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-45, GLYCOSYLATION AT ASN-42, FUNCTION, CATALYTIC ACTIVITY, MASS SPECTROMETRY. Tissue: Leaf.
[3]	"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: 15899692] [Abstract] Cited for: FUNCTION. Tissue: Leaf.
[4]	"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: 18704492] [Abstract] Cited for: DEVELOPMENTAL STAGE.
+	Additional computationally mapped references.

Cross-references

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3H5K	X-ray	1.45	A/B	1-261	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

3.2.2.22. 295871.

Family and domain databases

InterPro

IPR001574. Ribosome_inactivat_prot.
IPR017988. Ribosome_inactivat_prot_CS.
IPR016139. Ribosome_inactivat_prot_sub2.
IPR017989. Ribosome_inactivat_prot_subgr.
[Graphical view]

Gene3D

G3DSA:4.10.470.10. Ribosome_inactivat_prot_sub2. 1 hit.

Pfam

PF00161. RIP. 1 hit.
[Graphical view]

PRINTS

PR00396. SHIGARICIN.

PROSITE

PS00275. SHIGA_RICIN. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RIPL1_PHYDI

Accession

Primary (citable) accession number: P84853

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 16, 2006
Last sequence update:	February 10, 2009
Last modified:	January 19, 2010
This is version 25 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)