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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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei183 – 1831By similarity
Active sitei212 – 2121

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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi212 – 2121E → K: 10-fold reduction in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 23232 PublicationsAdd
BLAST
Chaini24 – 270247Ribosome-inactivating protein bryodin IPRO_0000030754Add
BLAST
Propeptidei271 – 29020Removed in mature formPRO_0000030755Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi214 – 2141N-linked (GlcNAc...)Sequence analysis
Glycosylationi250 – 2501N-linked (GlcNAc...)Sequence analysis

Post-translational modificationi

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

Keywords - PTMi

Glycoprotein

Structurei

Secondary structure

1
290
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi25 – 295Combined sources
Helixi34 – 4613Combined sources
Beta strandi50 – 545Combined sources
Beta strandi57 – 604Combined sources
Helixi66 – 694Combined sources
Beta strandi70 – 767Combined sources
Beta strandi82 – 887Combined sources
Turni89 – 913Combined sources
Beta strandi94 – 996Combined sources
Beta strandi102 – 1054Combined sources
Helixi109 – 1146Combined sources
Turni115 – 1173Combined sources
Beta strandi123 – 1275Combined sources
Helixi134 – 1418Combined sources
Helixi145 – 1473Combined sources
Helixi152 – 16312Combined sources
Helixi167 – 18014Combined sources
Helixi182 – 1865Combined sources
Helixi188 – 1969Combined sources
Beta strandi198 – 2003Combined sources
Helixi206 – 2138Combined sources
Helixi215 – 22511Combined sources
Turni226 – 2305Combined sources
Beta strandi231 – 2399Combined sources
Beta strandi245 – 2506Combined sources
Helixi254 – 2574Combined sources
Helixi266 – 2683Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BRYX-ray2.10Y/Z24-270[»]
ProteinModelPortaliP33185.
SMRiP33185. Positions 24-270.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti61 – 655RSSIS → LRHXI AA sequence (PubMed:2753596).Curated

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
EntryMethodResolution (Å)ChainPositionsPDBsum
1BRYX-ray2.10Y/Z24-270[»]
ProteinModelPortaliP33185.
SMRiP33185. Positions 24-270.
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: October 14, 2015
This is version 85 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.