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Protein

Ricin

Gene
N/A
Organism
Ricinus communis (Castor bean)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei50Carbohydrate; via amide nitrogen1
Binding sitei85Carbohydrate; via amide nitrogen1
Active sitei2121
Binding sitei324Carbohydrate; via carbonyl oxygenBy similarity1
Binding sitei349Carbohydrate1
Binding sitei354Carbohydrate1
Binding sitei360Carbohydrate1
Binding sitei409CarbohydrateBy similarity1
Binding sitei449CarbohydrateBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi115 – 116AMP2
Nucleotide bindingi156 – 158AMP3

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase, Protein synthesis inhibitor, Toxin
Biological processPlant defense
LigandLectin, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-18749
BRENDAi3.2.2.22 1204

Protein family/group databases

CAZyiCBM13 Carbohydrate-Binding Module Family 13
UniLectiniP02879

Names & Taxonomyi

Protein namesi
Recommended name:
Ricin
Cleaved into the following 3 chains:
Alternative name(s):
rRNA N-glycosidase
OrganismiRicinus communis (Castor bean)
Taxonomic identifieri3988 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsfabidsMalpighialesEuphorbiaceaeAcalyphoideaeAcalypheaeRicinus

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Pathology & Biotechi

Biotechnological usei

A deglycosylated A chain may be linked to monoclonal antibodies to produce immunotoxins exploited in cancer treatment. However, a point mutation should be introduced to eliminate vascular leak syndrome, a side effect resulting from endothelial damage.

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi83R → A: No effect on the toxic activity but suppresses the vascular leak syndrome. 1 Publication1
Mutagenesisi109L → A or M: No effect on the toxic activity or the vascular leak syndrome. 1 Publication1
Mutagenesisi110D → A, E or N: Suppresses the toxic activity. 1 Publication1
Mutagenesisi111V → A or M: No effect on the toxic activity or the vascular leak syndrome. 1 Publication1
Mutagenesisi132N → A: No effect on the toxic activity but Suppresses the vascular leak syndrome. 1 Publication1

Protein family/group databases

Allergomei2803 Ric c RIP

Chemistry databases

ChEMBLiCHEMBL4756

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 351 PublicationAdd BLAST35
ChainiPRO_000003074136 – 302Ricin A chainAdd BLAST267
PeptideiPRO_0000030742303 – 314Linker peptide1 PublicationAdd BLAST12
ChainiPRO_0000030743315 – 576Ricin B chainAdd BLAST262

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
GlycosylationiCAR_00008045N-linked (GlcNAc...) asparagine1 Publication1
GlycosylationiCAR_000081271N-linked (GlcNAc...) asparagine; partial1 Publication1
Disulfide bondi294 ↔ 318Interchain (between A and B chains)
Disulfide bondi334 ↔ 353
Disulfide bondi377 ↔ 394
Disulfide bondi465 ↔ 478
Disulfide bondi504 ↔ 521

Keywords - PTMi

Disulfide bond, Glycoprotein

PTM databases

GlyConnecti536
537
UniCarbKBiP02879

Interactioni

Subunit structurei

Disulfide-linked dimer of A and B chains.

Protein-protein interaction databases

BioGridi1022023, 2 interactors
DIPiDIP-46421N
IntActiP02879, 4 interactors
MINTiP02879

Chemistry databases

BindingDBiP02879

Structurei

Secondary structure

1576
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP02879
SMRiP02879
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP02879

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini321 – 448Ricin B-type lectin 1PROSITE-ProRule annotationAdd BLAST128
Repeati331 – 3731-alphaAdd BLAST43
Repeati374 – 4141-betaAdd BLAST41
Repeati417 – 4491-gammaAdd BLAST33
Domaini451 – 575Ricin B-type lectin 2PROSITE-ProRule annotationAdd BLAST125
Repeati462 – 4972-alphaAdd BLAST36
Repeati501 – 5402-betaAdd BLAST40
Repeati543 – 5702-gammaAdd BLAST28

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni43 – 45Carbohydrate bindingBy similarity3
Regioni176 – 181Carbohydrate binding6
Regioni230 – 232Carbohydrate binding3
Regioni336 – 340Carbohydrate binding5
Regioni548 – 551Carbohydrate binding4
Regioni565 – 569Carbohydrate binding5

Domaini

The B chain is composed of two domains, each domain consists of 3 homologous subdomains (alpha, beta, gamma).

Sequence similaritiesi

In the N-terminal section; belongs to the ribosome-inactivating protein family. Type 2 RIP subfamily.Curated

Keywords - Domaini

Repeat, Signal

Family and domain databases

CDDicd00161 RICIN, 2 hits
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
IPR017988 Ribosome_inactivat_prot_CS
IPR016138 Ribosome_inactivat_prot_sub1
IPR016139 Ribosome_inactivat_prot_sub2
IPR035992 Ricin_B-like_lectins
IPR000772 Ricin_B_lectin
PfamiView protein in Pfam
PF00652 Ricin_B_lectin, 2 hits
PF00161 RIP, 1 hit
PRINTSiPR00396 SHIGARICIN
SMARTiView protein in SMART
SM00458 RICIN, 2 hits
SUPFAMiSSF50370 SSF50370, 2 hits
SSF56371 SSF56371, 1 hit
PROSITEiView protein in PROSITE
PS50231 RICIN_B_LECTIN, 2 hits
PS00275 SHIGA_RICIN, 1 hit

Sequencei

Sequence statusi: Complete.

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

P02879-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKPGGNTIVI WMYAVATWLC FGSTSGWSFT LEDNNIFPKQ YPIINFTTAG
60 70 80 90 100
ATVQSYTNFI RAVRGRLTTG ADVRHEIPVL PNRVGLPINQ RFILVELSNH
110 120 130 140 150
AELSVTLALD VTNAYVVGYR AGNSAYFFHP DNQEDAEAIT HLFTDVQNRY
160 170 180 190 200
TFAFGGNYDR LEQLAGNLRE NIELGNGPLE EAISALYYYS TGGTQLPTLA
210 220 230 240 250
RSFIICIQMI SEAARFQYIE GEMRTRIRYN RRSAPDPSVI TLENSWGRLS
260 270 280 290 300
TAIQESNQGA FASPIQLQRR NGSKFSVYDV SILIPIIALM VYRCAPPPSS
310 320 330 340 350
QFSLLIRPVV PNFNADVCMD PEPIVRIVGR NGLCVDVRDG RFHNGNAIQL
360 370 380 390 400
WPCKSNTDAN QLWTLKRDNT IRSNGKCLTT YGYSPGVYVM IYDCNTAATD
410 420 430 440 450
ATRWQIWDNG TIINPRSSLV LAATSGNSGT TLTVQTNIYA VSQGWLPTNN
460 470 480 490 500
TQPFVTTIVG LYGLCLQANS GQVWIEDCSS EKAEQQWALY ADGSIRPQQN
510 520 530 540 550
RDNCLTSDSN IRETVVKILS CGPASSGQRW MFKNDGTILN LYSGLVLDVR
560 570
ASDPSLKQII LYPLHGDPNQ IWLPLF
Length:576
Mass (Da):64,091
Last modified:August 13, 1987 - v1
Checksum:iC14C4B77A8B5470D
GO

Sequence cautioni

The sequence described in Ref. 4 differs from that shown. High number of conflicts with the sequence translated from DNA.Curated
The sequence described in Ref. 5 differs from that shown. High number of conflicts with the sequence translated from DNA.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti76E → D in CAA26230 (PubMed:3838723).Curated1
Sequence conflicti551A → R in CAA26230 (PubMed:3838723).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03179 Genomic DNA Translation: CAA26939.1
X52908 Genomic DNA Translation: CAA37095.1
X02388 mRNA Translation: CAA26230.1
PIRiA24041 RLCSD
RefSeqiNP_001310630.1, NM_001323701.1

Genome annotation databases

GeneIDi8261245
KEGGircu:8261245

Similar proteinsi

Cross-referencesi

Web resourcesi

Protein Spotlight

Baneful beans - Issue 31 of February 2003

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03179 Genomic DNA Translation: CAA26939.1
X52908 Genomic DNA Translation: CAA37095.1
X02388 mRNA Translation: CAA26230.1
PIRiA24041 RLCSD
RefSeqiNP_001310630.1, NM_001323701.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BR5X-ray2.50A36-302[»]
1BR6X-ray2.30A36-302[»]
1IFSX-ray2.00A38-298[»]
1IFTX-ray1.80A38-298[»]
1IFUX-ray2.40A38-298[»]
1IL3X-ray2.80A36-302[»]
1IL4X-ray2.60A36-302[»]
1IL5X-ray2.80A/B36-302[»]
1IL9X-ray3.10A36-302[»]
1J1MX-ray1.50A36-302[»]
1OBSX-ray2.20A36-302[»]
1OBTX-ray2.80A36-302[»]
1RTCX-ray2.30A36-302[»]
1UQ4X-ray1.90A40-302[»]
1UQ5X-ray1.40A40-302[»]
2AAIX-ray2.50A36-302[»]
B315-576[»]
2P8NX-ray1.94A36-302[»]
2PJOX-ray1.80A36-302[»]
2R2XX-ray2.40A36-302[»]
2R3DX-ray2.09A36-302[»]
2VC3X-ray1.60A36-302[»]
2VC4X-ray1.39A36-302[»]
3BJGX-ray2.14A36-302[»]
3EJ5X-ray2.50X40-296[»]
3HIOX-ray2.00A36-302[»]
3LC9X-ray2.28A36-233[»]
3MK9X-ray2.08A36-233[»]
3PX8X-ray1.29X39-296[»]
3PX9X-ray1.89X39-296[»]
3RTIX-ray2.80A36-302[»]
B315-576[»]
3RTJX-ray3.00A36-302[»]
B315-576[»]
3SRPX-ray2.14A36-302[»]
4ESIX-ray1.87A36-302[»]
4HUOX-ray1.52X36-302[»]
4HUPX-ray1.70X36-302[»]
4HV3X-ray1.54A36-302[»]
4HV7X-ray1.87X36-302[»]
4IMVX-ray2.25A36-233[»]
4KUCX-ray2.79A/I36-302[»]
4LGPX-ray2.40A/C36-296[»]
4LGRX-ray1.65A40-294[»]
4LGSX-ray2.70A39-301[»]
4LHJX-ray1.80A39-297[»]
4LHQX-ray2.30A/C39-298[»]
4MX1X-ray1.59A36-302[»]
4MX5X-ray1.52X36-302[»]
4Q2VX-ray2.20A36-302[»]
4Z9KX-ray1.50A39-296[»]
5BOZX-ray3.10A/B/C/D/E/F39-299[»]
5DDZX-ray1.50A36-302[»]
5E1HX-ray2.03A40-297[»]
5GU4X-ray1.55A/B36-302[»]
5J56X-ray1.80A36-302[»]
5J57X-ray1.70A36-302[»]
5SV3X-ray2.73B/D36-233[»]
5U4LX-ray2.50A36-302[»]
5U4MX-ray2.50A40-294[»]
ProteinModelPortaliP02879
SMRiP02879
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi1022023, 2 interactors
DIPiDIP-46421N
IntActiP02879, 4 interactors
MINTiP02879

Chemistry databases

BindingDBiP02879
ChEMBLiCHEMBL4756

Protein family/group databases

Allergomei2803 Ric c RIP
CAZyiCBM13 Carbohydrate-Binding Module Family 13
UniLectiniP02879

PTM databases

GlyConnecti536
537
UniCarbKBiP02879

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi8261245
KEGGircu:8261245

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-18749
BRENDAi3.2.2.22 1204

Miscellaneous databases

EvolutionaryTraceiP02879
PROiPR:P02879

Family and domain databases

CDDicd00161 RICIN, 2 hits
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
IPR017988 Ribosome_inactivat_prot_CS
IPR016138 Ribosome_inactivat_prot_sub1
IPR016139 Ribosome_inactivat_prot_sub2
IPR035992 Ricin_B-like_lectins
IPR000772 Ricin_B_lectin
PfamiView protein in Pfam
PF00652 Ricin_B_lectin, 2 hits
PF00161 RIP, 1 hit
PRINTSiPR00396 SHIGARICIN
SMARTiView protein in SMART
SM00458 RICIN, 2 hits
SUPFAMiSSF50370 SSF50370, 2 hits
SSF56371 SSF56371, 1 hit
PROSITEiView protein in PROSITE
PS50231 RICIN_B_LECTIN, 2 hits
PS00275 SHIGA_RICIN, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRICI_RICCO
AccessioniPrimary (citable) accession number: P02879
Secondary accession number(s): P02880
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: August 13, 1987
Last modified: July 18, 2018
This is version 171 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. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Protein Spotlight
    Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
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