P84786 (RIP_DRIMA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Ribosome-inactivating protein charybdin EC=3.2.2.22 Alternative name(s): rRNA N-glycosidase
Organism	Drimia maritima (Sea squill) (Charybdis maritima)
Taxonomic identifier	82070 [NCBI]
Taxonomic lineage	Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Asparagales › Hyacinthaceae › Urgineoideae › Charybdis

Protein attributes

Sequence length	257 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Inhibits translation in rabbit reticulocytes. Ref.1
Catalytic activity	Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA. Ref.1
Sequence similarities	Belongs to the ribosome-inactivating protein family. Type 1 RIP subfamily. Ref.1

Ontologies

Keywords
Biological process	Plant defense
Molecular function	Hydrolase Protein synthesis inhibitor Toxin
PTM	Disulfide bond
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

Chain

1 – 257

257

Ribosome-inactivating protein charybdin

PRO_0000248258

Sites

Active site

167

1

Ref.1

Site

79

1

Important for catalytic activity Ref.1

Site

117

1

Important for catalytic activity Ref.1

Site

170

1

Important for catalytic activity Ref.1

Amino acid modifications

Disulfide bond

217 ↔ 254

Ref.1

Secondary structure

1

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257

Helix Strand Turn

Details...

Beta strand

7 – 16

10

Helix

21 – 35

15

Beta strand

37 – 40

4

Beta strand

43 – 45

3

Beta strand

56 – 64

9

Beta strand

67 – 74

8

Turn

75 – 77

3

Beta strand

80 – 84

5

Beta strand

86 – 88

3

Beta strand

91 – 93

3

Helix

117 – 124

8

Helix

128 – 130

3

Helix

135 – 147

13

Helix

151 – 164

14

Helix

166 – 170

5

Helix

172 – 180

9

Turn

181 – 183

3

Helix

192 – 196

5

Helix

199 – 201

3

Helix

202 – 214

13

Beta strand

223 – 225

3

Beta strand

228 – 230

3

Helix

233 – 237

5

Beta strand

240 – 243

4

Helix

247 – 250

4

Sequences

	Sequence		Length	Mass (Da)
	P84786 [UniParc]. Last modified September 5, 2006. Version 1. Checksum: 12EB2E35328175AE	FASTA	257	29,252
	10 20 30 40 50 60 SQCKAMTVKF TVELDIERLT GQTYTDFIKN LRRSLATWYL HGVPVLPLYN QEADPRGFDL 70 80 90 100 110 120 KLTFRGQVTT VRIHRDDLVL RGYQMQGAGK WLELERPSTQ TGHLIEGSEL LEFGPSYEEL 130 140 150 160 170 180 AAAAQQDILD ISYNKNALQD AVSKLAVSTN TRDRARSLIV VSQMFCEATR FVDIANHFAF 190 200 210 220 230 240 NLESSEPVKL PQWMQNDLEK NWVRFSFMIL KSNADPCYKF EPQTIYGKII KTADELLNFL 250 GIVEQHPDTR SPPCAAG

References

[1]

"Isolation, characterization, sequencing and crystal structure of charybdin, a type 1 ribosome-inactivating protein from Charybdis maritima agg." Touloupakis E., Gessmann R., Kavelaki K., Christofakis E., Petratos K., Ghanotakis D.F. FEBS J. 273:2684-2692(2006) [PubMed: 16817896] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-14 AND 242-257, NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 4-252, X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY. Tissue: Bulb.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

DQ323742 Genomic DNA. No translation available.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2B7U	X-ray	1.60	A	1-257	[»]

ProteinModelPortal

P84786.

SMR

P84786. Positions 4-257.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR001574. Ribosome_inactivat_prot.
IPR016138. Ribosome_inactivat_prot_sub1.
IPR017989. Ribosome_inactivat_prot_subgr.
[Graphical view]

Gene3D

G3DSA:3.40.420.10. Ribosome_inactivat_prot_sub1. 1 hit.

Pfam

PF00161. RIP. 1 hit.
[Graphical view]

PRINTS

PR00396. SHIGARICIN.

SUPFAM

SSF56371. Ribosome_inactivat_prot. 1 hit.

PROSITE

PS00275. SHIGA_RICIN. False negative.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RIP_DRIMA

Accession

Primary (citable) accession number: P84786

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 5, 2006
Last sequence update:	September 5, 2006
Last modified:	October 19, 2011
This is version 25 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program