Reviewed, UniProtKB/Swiss-Prot P84854 (RIPL2_PHYDI)

Names and origin

Protein names	Recommended name:     Ribosome-inactivating protein PD-L3/PD-L4     EC=3.2.2.22 Alternative name(s):     rRNA N-glycosidase PD-L3/PD-L4
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.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Inhibits protein synthesis. Does not cleave supercoiled pBR322 dsDNA. Ref.3 Ref.4
Catalytic activity	Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA. Ref.3
Developmental stage	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. Ref.5
Miscellaneous	2 forms exist, PD-L3 and PD-L4, that differ in their post-translational modifications. PD-L4 is not glycosylated.
Sequence similarities	Belongs to the ribosome-inactivating protein family. Type 1 RIP subfamily.
Mass spectrometry	Molecular mass is 30356±1 Da from positions 1 - 261. Determined by ESI. PD-L3. Ref.3 Molecular mass is 29185±1 Da from positions 1 - 261. Determined by ESI. PD-L4. Ref.3 Molecular mass is 30357.7 Da from positions 1 - 261. Determined by ESI. PD-L3. Ref.2

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.3 Inferred from direct assay. Source: UniProtKB negative regulation of translation Ref.3 Inferred from direct assay. Source: UniProtKB pathogenesis Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	rRNA N-glycosylase activity Ref.3 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-L3/PD-L4

PRO_0000235848

Sites

Active site

175

1

By similarity

Amino acid modifications

Glycosylation

10

1

N-linked (GlcNAc...); in PD-L3 Ref.3 Ref.2

Disulfide bond

34 ↔ 258

By similarity

Disulfide bond

84 ↔ 105

By similarity

Experimental info

Mutagenesis

211

1

S → A: Reduces activity on DNA, rRNA and poly(A). Does not affect activity on ribosomes or inhibition of protein synthesis. Ref.1 Ref.6

Secondary structure

1

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261

Helix Strand Turn

Details...

Beta strand

3 – 8

6

Helix

13 – 27

15

Beta strand

37 – 39

3

Beta strand

45 – 47

3

Beta strand

49 – 55

7

Beta strand

61 – 67

7

Turn

68 – 70

3

Beta strand

73 – 80

8

Beta strand

83 – 88

6

Helix

94 – 104

11

Beta strand

110 – 113

4

Helix

122 – 129

8

Helix

134 – 136

3

Helix

141 – 151

11

Helix

159 – 178

20

Helix

180 – 188

9

Turn

189 – 191

3

Helix

198 – 216

19

Beta strand

221 – 229

9

Beta strand

235 – 240

6

Helix

241 – 244

4

Helix

245 – 247

3

Sequences

	Sequence		Length	Mass (Da)
	P84854-1 [UniParc]. Last modified May 29, 2007. Version 2. Checksum: D497355FC3B7C463	FASTA	261	29,190
	10 20 30 40 50 60 VNTITFDVGN ATINKYATFM ESLRNEAKDP TLKCYGIPML PDSNLTPKYV LVKLQDASSK 70 80 90 100 110 120 TITLMLRRNN LYVMGYSDLY NGKCRYHIFN DISSTESTDV ENTLCPNSNS REKKAINYNS 130 140 150 160 170 180 QYSTLQNKAG VSSRSQVQLG IQILNSDIGK ISGVSTFTDK TEAEFLLVAI QMVSEAARFK 190 200 210 220 230 240 YIENQVKTNF NRAFNPNPKV LSLEENWGKI SLAIHNAKNG ALTSPLELKN ADDTKWIVLR 250 260 VDEIKPDMGL LNYVSGTCQT T

References

[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: 17243169] [Abstract] Cited for: PROTEIN SEQUENCE, MUTAGENESIS OF SER-211. Tissue: Leaf.
[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: 19014994] [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: 10213004] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-45, GLYCOSYLATION AT ASN-10, FUNCTION, CATALYTIC ACTIVITY, MASS SPECTROMETRY. Tissue: Leaf.
[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: 15899692] [Abstract] Cited for: FUNCTION. Tissue: Leaf.
[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: 18704492] [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: 17963235] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.10 ANGSTROMS) IN COMPLEX WITH ADENINE, MUTAGENESIS OF SER-211.

Cross-references

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2QES	X-ray	1.24	A	1-261	[»]
2QET	X-ray	1.24	A	1-261	[»]
2Z4U	X-ray	1.10	A	1-261	[»]
2Z53	X-ray	1.29	A	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

RIPL2_PHYDI

Accession

Primary (citable) accession number: P84854

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 16, 2006
Last sequence update:	May 29, 2007
Last modified:	April 14, 2009
This is version 22 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)