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Protein

Ribosome-inactivating protein bryodin I

Gene
N/A
Organism
Bryonia dioica (Red bryony) (Bryonia cretica subsp. dioica)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Ribosome-inactivating protein of type 1, inhibits protein synthesis in animal cells.

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei183By similarity1
Active sitei2121

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protein synthesis inhibitor, Toxin

Keywords - Biological processi

Plant defense

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosome-inactivating protein bryodin I (EC:3.2.2.22)
Alternative name(s):
BD1
rRNA N-glycosidase
OrganismiBryonia dioica (Red bryony) (Bryonia cretica subsp. dioica)
Taxonomic identifieri3652 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsfabidsCucurbitalesCucurbitaceaeBryonieaeBryonia

Pathology & Biotechi

Biotechnological usei

Especially useful as immunotoxin for pharmacological applications as it has low toxicity in rats and mice but is potent once inside target cells.

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi212E → K: 10-fold reduction in activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 232 PublicationsAdd BLAST23
ChainiPRO_000003075424 – 270Ribosome-inactivating protein bryodin IAdd BLAST247
PropeptideiPRO_0000030755271 – 290Removed in mature formAdd BLAST20

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi214N-linked (GlcNAc...)Sequence analysis1
Glycosylationi250N-linked (GlcNAc...)Sequence analysis1

Post-translational modificationi

Appears to undergo proteolytic cleavage in the C-terminal to produce a shorter protein.

Keywords - PTMi

Glycoprotein

Structurei

Secondary structure

1290
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi25 – 29Combined sources5
Helixi34 – 46Combined sources13
Beta strandi50 – 54Combined sources5
Beta strandi57 – 60Combined sources4
Helixi66 – 69Combined sources4
Beta strandi70 – 76Combined sources7
Beta strandi82 – 88Combined sources7
Turni89 – 91Combined sources3
Beta strandi94 – 99Combined sources6
Beta strandi102 – 105Combined sources4
Helixi109 – 114Combined sources6
Turni115 – 117Combined sources3
Beta strandi123 – 127Combined sources5
Helixi134 – 141Combined sources8
Helixi145 – 147Combined sources3
Helixi152 – 163Combined sources12
Helixi167 – 180Combined sources14
Helixi182 – 186Combined sources5
Helixi188 – 196Combined sources9
Beta strandi198 – 200Combined sources3
Helixi206 – 213Combined sources8
Helixi215 – 225Combined sources11
Turni226 – 230Combined sources5
Beta strandi231 – 239Combined sources9
Beta strandi245 – 250Combined sources6
Helixi254 – 257Combined sources4
Helixi266 – 268Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BRYX-ray2.10Y/Z24-270[»]
ProteinModelPortaliP33185.
SMRiP33185.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP33185.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Signal

Family and domain databases

Gene3Di3.40.420.10. 1 hit.
4.10.470.10. 1 hit.
InterProiIPR001574. 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]
PfamiPF00161. RIP. 1 hit.
[Graphical view]
PRINTSiPR00396. SHIGARICIN.
SUPFAMiSSF56371. SSF56371. 1 hit.
PROSITEiPS00275. SHIGA_RICIN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P33185-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIKLLVLWLL ILTIFLKSPT VEGDVSFRLS GATTTSYGVF IKNLREALPY
60 70 80 90 100
ERKVYNIPLL RSSISGSGRY TLLHLTNYAD ETISVAVDVT NVYIMGYLAG
110 120 130 140 150
DVSYFFNEAS ATEAAKFVFK DAKKKVTLPY SGNYERLQTA AGKIRENIPL
160 170 180 190 200
GLPALDSAIT TLYYYTASSA ASALLVLIQS TAESARYKFI EQQIGKRVDK
210 220 230 240 250
TFLPSLATIS LENNWSALSK QIQIASTNNG QFESPVVLID GNNQRVSITN
260 270 280 290
ASARVVTSNI ALLLNRNNIA AIGEDISMTL IGFEHGLYGI
Length:290
Mass (Da):31,789
Last modified:December 1, 2000 - v3
Checksum:iE966CD9C031A42DB
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti61 – 65RSSIS → LRHXI AA sequence (PubMed:2753596).Curated5

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
I24020 Unassigned DNA. No translation available.
PIRiS16491.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
I24020 Unassigned DNA. No translation available.
PIRiS16491.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BRYX-ray2.10Y/Z24-270[»]
ProteinModelPortaliP33185.
SMRiP33185.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP33185.

Family and domain databases

Gene3Di3.40.420.10. 1 hit.
4.10.470.10. 1 hit.
InterProiIPR001574. 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]
PfamiPF00161. RIP. 1 hit.
[Graphical view]
PRINTSiPR00396. SHIGARICIN.
SUPFAMiSSF56371. SSF56371. 1 hit.
PROSITEiPS00275. SHIGA_RICIN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRIP1_BRYDI
AccessioniPrimary (citable) accession number: P33185
Secondary accession number(s): Q9S8I9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: December 1, 2000
Last modified: November 30, 2016
This is version 87 of the entry and version 3 of the sequence. [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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.