P20656 (RIP6_SAPOF) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribosome-inactivating protein saporin-6
Short name=SAP-6
Short name=SO-6
EC=3.2.2.22

Alternative name(s):
rRNA N-glycosidase

Gene names

Name:

SAP6

Organism

Saponaria officinalis (Common soapwort) (Lychnis saponaria)

Taxonomic identifier

3572 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › Caryophyllales › Caryophyllaceae › Saponaria

Protein attributes

Sequence length	299 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Ribosome-inactivating protein of type 1, inhibits protein synthesis in animal cells. Useful as immunotoxin for pharmacological applications.
Catalytic activity	Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
Tissue specificity	Seeds and leaves of the plant.
Sequence similarities	Belongs to the ribosome-inactivating protein family. Type 1 RIP subfamily.

Ontologies

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

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 24

24

Ref.1 Ref.4 Ref.5

Chain

25 – 277

253

Ribosome-inactivating protein saporin-6

PRO_0000030776

Propeptide

278 – 299

22

Potential

PRO_0000030777

Sites

Active site

200

1

Ref.6

Amino acid modifications

Glycosylation

283

1

N-linked (GlcNAc...) Potential

Natural variations

Natural variant

72

1

E → D.

Natural variant

115

1

R → K.

Experimental info

Sequence conflict

60

1

G → S AA sequence Ref.4

Sequence conflict

123

1

S → L Ref.2

Sequence conflict

123

1

S → L Ref.5

Sequence conflict

212

1

I → T AA sequence Ref.1

Secondary structure

1

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299

Helix Strand Turn

Details...

Beta strand

26 – 31

6

Helix

40 – 51

12

Beta strand

74 – 80

7

Beta strand

86 – 88

3

Turn

92 – 94

3

Beta strand

99 – 103

5

Beta strand

109 – 113

5

Turn

115 – 117

3

Helix

120 – 126

7

Helix

132 – 134

3

Beta strand

135 – 137

3

Helix

144 – 151

8

Helix

160 – 162

3

Helix

168 – 175

8

Turn

176 – 179

4

Helix

184 – 196

13

Helix

199 – 203

5

Helix

205 – 213

9

Turn

214 – 216

3

Helix

223 – 230

8

Helix

232 – 239

8

Beta strand

248 – 250

3

Helix

262 – 265

4

Sequences

	Sequence		Length	Mass (Da)
	P20656 [UniParc]. Last modified October 1, 1996. Version 2. Checksum: 4BC312958BB4E79B	FASTA	299	33,607
	10 20 30 40 50 60 MKIYVVATIA WILLQFSAWT TTDAVTSITL DLVNPTAGQY SSFVDKIRNN VKDPNLKYGG 70 80 90 100 110 120 TDIAVIGPPS KEKFLRINFQ SSRGTVSLGL KRDNLYVVAY LAMDNTNVNR AYYFRSEITS 130 140 150 160 170 180 AESTALFPEA TTANQKALEY TEDYQSIEKN AQITQGDQSR KELGLGIDLL STSMEAVNKK 190 200 210 220 230 240 ARVVKDEARF LLIAIQMTAE AARFRYIQNL VIKNFPNKFN SENKVIQFEV NWKKISTAIY 250 260 270 280 290 GDAKNGVFNK DYDFGFGKVR QVKDLQMGLL MYLGKPKSSN EANSTVRHYG PLKPTLLIT

References

[1]	"Nucleotide sequence of cDNA coding for saporin-6, a type-1 ribosome-inactivating protein from Saponaria officinalis." Benatti L., Saccardo M.B., Dani M., Nitti G., Sassano M., Lorenzetti R., Lappi D.A., Soria M. Eur. J. Biochem. 183:465-470(1989) [PubMed: 2547612] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-283, PROTEIN SEQUENCE OF 25-115; 206-213 AND 234-277. Tissue: Leaf.
[2]	"The expression of saporin, a ribosome-inactivating protein from the plant Saponaria officinalis, in Escherichia coli." Barthelemy I., Martineau D., Ong M., Matsunami R., Ling N., Benatti L., Cavallaro U., Soria M., Lappi D.A. J. Biol. Chem. 268:6541-6548(1993) [PubMed: 8454624] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 25-277.
[3]	"A Saporin-6 cDNA containing a precursor sequence coding for a carboxyl-terminal extension." Benatti L., Nitti G., Solinas M., Valsasina B., Vitale A., Ceriotti A., Soria M.R. FEBS Lett. 291:285-288(1991) [PubMed: 1936274] [Abstract] Cited for: NUCLEOTIDE SEQUENCE OF 275-299. Tissue: Leaf.
[4]	"Characterization of a Saponaria officinalis seed ribosome-inactivating protein: immunoreactivity and sequence homologies." Lappi D.A., Esch F.S., Barbieri L., Stirpe F., Soria M. Biochem. Biophys. Res. Commun. 129:934-942(1985) [PubMed: 3925952] [Abstract] Cited for: PROTEIN SEQUENCE OF 25-61.
[5]	"Synthesis of saporin gene probes from partial protein sequence data: use of inosine-oligonucleotides, genomic DNA and the polymerase chain reaction." Fordham-Skelton A.P., Yarwood A., Croy R.R.D. Mol. Gen. Genet. 221:134-138(1990) [PubMed: 2325629] [Abstract] Cited for: PROTEIN SEQUENCE OF 25-72 AND 114-154.
[6]	"The crystal structure of saporin SO6 from Saponaria officinalis and its interaction with the ribosome." Savino C., Federici L., Ippoliti R., Lendaro E., Tsernoglou D. FEBS Lett. 470:239-243(2000) [PubMed: 10745075] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 25-277, ACTIVE SITE.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X15655 mRNA. Translation: CAA33685.1.
S57638 mRNA. Translation: AAB25863.1.
X69135 Genomic DNA. Translation: CAA48889.1.
X64917 mRNA. Translation: CAA46110.1.

PIR

S05205.
S16487.
S18307.
S29931.
S38527.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QI7	X-ray	2.00	A	25-277	[»]

ProteinModelPortal

P20656.

SMR

P20656. Positions 25-277.

ModBase

Search...

Protein family/group databases

Allergome

2805. Sap o RIP.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR001574. 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]

Gene3D

G3DSA:3.40.420.10. Ribosome_inactivat_prot_sub1. 1 hit.
G3DSA:4.10.470.10. Ribosome_inactivat_prot_sub2. 1 hit.

Pfam

PF00161. RIP. 1 hit.
[Graphical view]

PRINTS

PR00396. SHIGARICIN.

SUPFAM

SSF56371. Ribosome_inactivat_prot. 1 hit.

PROSITE

PS00275. SHIGA_RICIN. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RIP6_SAPOF

Accession

Primary (citable) accession number: P20656
Secondary accession number(s): Q41392

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1991
Last sequence update:	October 1, 1996
Last modified:	June 28, 2011
This is version 83 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program