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Protein

Ribosome-inactivating protein charybdin

Gene
N/A
Organism
Drimia maritima (Sea squill) (Charybdis maritima)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Inhibits translation in rabbit reticulocytes.1 Publication

Catalytic activityi

Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei79Important for catalytic activity1 Publication1
Sitei117Important for catalytic activity1 Publication1
Active sitei1671 Publication1
Sitei170Important for catalytic activity1 Publication1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase, Protein synthesis inhibitor, Toxin
Biological processPlant defense

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosome-inactivating protein charybdin (EC:3.2.2.22)
Alternative name(s):
rRNA N-glycosidase
OrganismiDrimia maritima (Sea squill) (Charybdis maritima)
Taxonomic identifieri82070 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaAsparagalesHyacinthaceaeUrgineoideaeDrimia

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002482581 – 257Ribosome-inactivating protein charybdinAdd BLAST257

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi217 ↔ 2541 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiP84786

Structurei

Secondary structure

1257
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi7 – 16Combined sources10
Helixi21 – 35Combined sources15
Beta strandi37 – 40Combined sources4
Beta strandi43 – 45Combined sources3
Beta strandi56 – 64Combined sources9
Beta strandi67 – 74Combined sources8
Turni75 – 77Combined sources3
Beta strandi80 – 84Combined sources5
Beta strandi86 – 88Combined sources3
Beta strandi91 – 93Combined sources3
Helixi117 – 124Combined sources8
Helixi128 – 130Combined sources3
Helixi135 – 147Combined sources13
Helixi151 – 164Combined sources14
Helixi166 – 170Combined sources5
Helixi172 – 180Combined sources9
Turni181 – 183Combined sources3
Helixi192 – 196Combined sources5
Helixi199 – 201Combined sources3
Helixi202 – 214Combined sources13
Beta strandi223 – 225Combined sources3
Beta strandi228 – 230Combined sources3
Helixi233 – 237Combined sources5
Beta strandi240 – 243Combined sources4
Helixi247 – 250Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2B7UX-ray1.60A1-257[»]
ProteinModelPortaliP84786
SMRiP84786
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP84786

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosome-inactivating protein family. Type 1 RIP subfamily.1 Publication

Family and domain databases

Gene3Di3.40.420.10, 1 hit
4.10.470.10, 1 hit
InterProiView protein in InterPro
IPR036041 Ribosome-inact_prot_sf
IPR017989 Ribosome_inactivat_1/2
IPR001574 Ribosome_inactivat_prot
IPR016138 Ribosome_inactivat_prot_sub1
IPR016139 Ribosome_inactivat_prot_sub2
PfamiView protein in Pfam
PF00161 RIP, 1 hit
PRINTSiPR00396 SHIGARICIN
SUPFAMiSSF56371 SSF56371, 1 hit

Sequencei

Sequence statusi: Complete.

P84786-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
SQCKAMTVKF TVELDIERLT GQTYTDFIKN LRRSLATWYL HGVPVLPLYN
60 70 80 90 100
QEADPRGFDL KLTFRGQVTT VRIHRDDLVL RGYQMQGAGK WLELERPSTQ
110 120 130 140 150
TGHLIEGSEL LEFGPSYEEL AAAAQQDILD ISYNKNALQD AVSKLAVSTN
160 170 180 190 200
TRDRARSLIV VSQMFCEATR FVDIANHFAF NLESSEPVKL PQWMQNDLEK
210 220 230 240 250
NWVRFSFMIL KSNADPCYKF EPQTIYGKII KTADELLNFL GIVEQHPDTR

SPPCAAG
Length:257
Mass (Da):29,252
Last modified:September 5, 2006 - v1
Checksum:i12EB2E35328175AE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ323742 Genomic DNA No translation available.

Entry informationi

Entry nameiRIP_DRIMA
AccessioniPrimary (citable) accession number: P84786
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 5, 2006
Last sequence update: September 5, 2006
Last modified: May 23, 2018
This is version 44 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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