Reviewed, UniProtKB/Swiss-Prot P33185 (RIP1_BRYDI)

Names and origin

Protein names	Recommended name:     Ribosome-inactivating protein bryodin I     EC=3.2.2.22 Alternative name(s):     rRNA N-glycosidase     BD1
Organism	Bryonia dioica (Red bryony)
Taxonomic identifier	3652 [NCBI]
Taxonomic lineage	Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids I › Cucurbitales › Cucurbitaceae › Bryonia

Protein attributes

Sequence length	290 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.
Catalytic activity	Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
Post-translational modification	Appears to undergo proteolytic cleavage in the C-terminal to produce a shorter protein.
Biotechnological use	Especially useful as immunotoxin for pharmacological applications as it has low toxicity in rats and mice but is potent once inside target cells.
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 pathogenesis 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 – 23

23

Ref.3 Ref.4

Chain

24 – 270

247

Ribosome-inactivating protein bryodin I

PRO_0000030754

Propeptide

271 – 290

20

Removed in mature form

PRO_0000030755

Sites

Active site

183

1

By similarity

Active site

212

1

Amino acid modifications

Glycosylation

214

1

N-linked (GlcNAc...) Potential

Glycosylation

250

1

N-linked (GlcNAc...) Potential

Experimental info

Mutagenesis

212

1

E → K: 10-fold reduction in activity. Ref.1

Sequence conflict

61 – 65

5

RSSIS → LRHXI AA sequence Ref.3

Secondary structure

1

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290

Helix Strand Turn

Details...

Beta strand

25 – 29

5

Helix

34 – 46

13

Beta strand

50 – 54

5

Beta strand

57 – 60

4

Helix

66 – 69

4

Beta strand

70 – 76

7

Beta strand

82 – 88

7

Turn

89 – 91

3

Beta strand

94 – 99

6

Beta strand

102 – 105

4

Helix

109 – 114

6

Turn

115 – 117

3

Beta strand

123 – 127

5

Helix

134 – 141

8

Helix

145 – 147

3

Helix

152 – 163

12

Helix

167 – 180

14

Helix

182 – 186

5

Helix

188 – 196

9

Beta strand

198 – 200

3

Helix

206 – 213

8

Helix

215 – 225

11

Turn

226 – 230

5

Beta strand

231 – 239

9

Beta strand

245 – 250

6

Helix

254 – 257

4

Helix

266 – 268

3

Sequences

	Sequence		Length	Mass (Da)
	P33185-1 [UniParc]. Last modified December 1, 2000. Version 3. Checksum: E966CD9C031A42DB	FASTA	290	31,789
	10 20 30 40 50 60 MIKLLVLWLL ILTIFLKSPT VEGDVSFRLS GATTTSYGVF IKNLREALPY ERKVYNIPLL 70 80 90 100 110 120 RSSISGSGRY TLLHLTNYAD ETISVAVDVT NVYIMGYLAG DVSYFFNEAS ATEAAKFVFK 130 140 150 160 170 180 DAKKKVTLPY SGNYERLQTA AGKIRENIPL GLPALDSAIT TLYYYTASSA ASALLVLIQS 190 200 210 220 230 240 TAESARYKFI EQQIGKRVDK TFLPSLATIS LENNWSALSK QIQIASTNNG QFESPVVLID 250 260 270 280 290 GNNQRVSITN ASARVVTSNI ALLLNRNNIA AIGEDISMTL IGFEHGLYGI

References

[1]	"Molecular, biological, and preliminary structural analysis of recombinant bryodin 1, a ribosome-inactivating protein from the plant Bryonia dioica." Gawlak S.L., Neubauer M., Klei H.E., Chang C.Y.Y., Einspahr H.M., Siegall C.B. Biochemistry 36:3095-3103(1997) [PubMed: 9115985] [Abstract] Cited for: NUCLEOTIDE SEQUENCE, MUTAGENESIS OF GLU-212, X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS). Tissue: Leaf.
[2]	"Cloning and expression of a gene encoding bryodin 1 from Bryonia dioica." Siegall C.B. Patent number US5541110, 30-JUL-1996 Cited for: NUCLEOTIDE SEQUENCE.
[3]	"N-terminal sequence of some ribosome-inactivating proteins." Montecucchi P.-C., Lazzarini A.M., Barbieri L., Stirpe F., Soria M., Lappi D. Int. J. Pept. Protein Res. 33:263-267(1989) [PubMed: 2753596] [Abstract] Cited for: PROTEIN SEQUENCE OF 24-66. Tissue: Seed.
[4]	"Characterization of ribosome-inactivating proteins isolated from Bryonia dioica and their utility as carcinoma-reactive immunoconjugates." Siegall C.B., Gawlak S.L., Chace D., Wolff E.A., Mixan B., Marquardt H. Bioconj. Chem. 5:423-429(1994) [PubMed: 7849072] [Abstract] Cited for: PROTEIN SEQUENCE OF 24-43. Tissue: Root.

Cross-references

Sequence databases

EMBLGenBankDDBJ

I24020 Unassigned DNA. No translation available.

PIR

S16491.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BRY	X-ray	2.10	Y/Z	24-270	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

3.2.2.22. 256122.

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.

PROSITE

PS00275. SHIGA_RICIN. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RIP1_BRYDI

Accession

Primary (citable) accession number: P33185
Secondary accession number(s): Q9S8I9

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	December 1, 2000
Last modified:	June 16, 2009
This is version 67 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)