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P02879 (RICI_RICCO) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 146. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ricin

Cleaved into the following 3 chains:

  1. Ricin A chain
    EC=3.2.2.22
    Alternative name(s):
    rRNA N-glycosidase
  2. Linker peptide
  3. Ricin B chain
OrganismRicinus communis (Castor bean)
Taxonomic identifier3988 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsfabidsMalpighialesEuphorbiaceaeAcalyphoideaeAcalypheaeRicinus

Protein attributes

Sequence length576 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

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

Subunit structure

Disulfide-linked dimer of A and B chains.

Domain

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

Biotechnological use

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.

Sequence similarities

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

Contains 2 ricin B-type lectin domains.

Sequence caution

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

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

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 3535 Ref.4
Chain36 – 302267Ricin A chain
PRO_0000030741
Peptide303 – 31412Linker peptide
PRO_0000030742
Chain315 – 576262Ricin B chain
PRO_0000030743

Regions

Domain321 – 448128Ricin B-type lectin 1
Repeat331 – 373431-alpha
Repeat374 – 414411-beta
Repeat417 – 449331-gamma
Domain451 – 575125Ricin B-type lectin 2
Repeat462 – 497362-alpha
Repeat501 – 540402-beta
Repeat543 – 570282-gamma
Nucleotide binding115 – 1162AMP
Nucleotide binding156 – 1583AMP
Region43 – 453Carbohydrate binding By similarity
Region176 – 1816Carbohydrate binding
Region230 – 2323Carbohydrate binding
Region336 – 3405Carbohydrate binding
Region548 – 5514Carbohydrate binding
Region565 – 5695Carbohydrate binding

Sites

Active site2121
Binding site501Carbohydrate; via amide nitrogen
Binding site851Carbohydrate; via amide nitrogen
Binding site3241Carbohydrate; via carbonyl oxygen By similarity
Binding site3491Carbohydrate
Binding site3541Carbohydrate
Binding site3601Carbohydrate
Binding site4091Carbohydrate By similarity
Binding site4491Carbohydrate By similarity

Amino acid modifications

Glycosylation451N-linked (GlcNAc...) Ref.6
CAR_000080
Glycosylation2711N-linked (GlcNAc...); partial Ref.6
CAR_000081
Glycosylation4091N-linked (GlcNAc...)
Glycosylation4491N-linked (GlcNAc...)
Disulfide bond294 ↔ 318Interchain (between A and B chains)
Disulfide bond334 ↔ 353
Disulfide bond377 ↔ 394
Disulfide bond465 ↔ 478
Disulfide bond504 ↔ 521

Experimental info

Mutagenesis831R → A: No effect on the toxic activity but suppresses the vascular leak syndrome. Ref.15
Mutagenesis1091L → A or M: No effect on the toxic activity or the vascular leak syndrome. Ref.15
Mutagenesis1101D → A, E or N: Suppresses the toxic activity. Ref.15
Mutagenesis1111V → A or M: No effect on the toxic activity or the vascular leak syndrome. Ref.15
Mutagenesis1321N → A: No effect on the toxic activity but Suppresses the vascular leak syndrome. Ref.15
Sequence conflict761E → D in CAA26230. Ref.3
Sequence conflict5511A → R in CAA26230. Ref.3

Secondary structure

................................................................................................................ 576
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P02879 [UniParc].

Last modified August 13, 1987. Version 1.
Checksum: C14C4B77A8B5470D

FASTA57664,091
        10         20         30         40         50         60 
MKPGGNTIVI WMYAVATWLC FGSTSGWSFT LEDNNIFPKQ YPIINFTTAG ATVQSYTNFI 

        70         80         90        100        110        120 
RAVRGRLTTG ADVRHEIPVL PNRVGLPINQ RFILVELSNH AELSVTLALD VTNAYVVGYR 

       130        140        150        160        170        180 
AGNSAYFFHP DNQEDAEAIT HLFTDVQNRY TFAFGGNYDR LEQLAGNLRE NIELGNGPLE 

       190        200        210        220        230        240 
EAISALYYYS TGGTQLPTLA RSFIICIQMI SEAARFQYIE GEMRTRIRYN RRSAPDPSVI 

       250        260        270        280        290        300 
TLENSWGRLS TAIQESNQGA FASPIQLQRR NGSKFSVYDV SILIPIIALM VYRCAPPPSS 

       310        320        330        340        350        360 
QFSLLIRPVV PNFNADVCMD PEPIVRIVGR NGLCVDVRDG RFHNGNAIQL WPCKSNTDAN 

       370        380        390        400        410        420 
QLWTLKRDNT IRSNGKCLTT YGYSPGVYVM IYDCNTAATD ATRWQIWDNG TIINPRSSLV 

       430        440        450        460        470        480 
LAATSGNSGT TLTVQTNIYA VSQGWLPTNN TQPFVTTIVG LYGLCLQANS GQVWIEDCSS 

       490        500        510        520        530        540 
EKAEQQWALY ADGSIRPQQN RDNCLTSDSN IRETVVKILS CGPASSGQRW MFKNDGTILN 

       550        560        570 
LYSGLVLDVR ASDPSLKQII LYPLHGDPNQ IWLPLF 

« Hide

References

[1]"Genomic cloning and characterization of a ricin gene from Ricinus communis."
Halling K.C., Halling A.C., Murray E.E., Ladin B.F., Houston L.L., Weaver R.F.
Nucleic Acids Res. 13:8019-8033(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The lectin gene family of Ricinus communis: cloning of a functional ricin gene and three lectin pseudogenes."
Tregear J.W., Roberts L.M.
Plant Mol. Biol. 18:515-525(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"Nucleotide sequence of cloned cDNA coding for preproricin."
Lamb A., Roberts L.M., Lord J.M.
Eur. J. Biochem. 148:265-270(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 12-576.
[4]"Isolation and sequences of peptic peptides, and the complete sequence of Ile chain of ricin-D."
Yoshitake S., Funatsu G., Funatsu M.
Agric. Biol. Chem. 42:1267-1274(1978)
Cited for: PROTEIN SEQUENCE OF 36-302.
[5]"Primary structure of Ala chain of ricin D."
Funatsu G., Kimura M., Funatsu M.
Agric. Biol. Chem. 43:2221-2224(1979) [AGRICOLA] [Europe PMC]
Cited for: PROTEIN SEQUENCE OF 315-576.
[6]"Structural analyses of sugar chains from ricin A-chain variant."
Kimura Y., Kusuoku H., Tada M., Takagi S., Funatsu G.
Agric. Biol. Chem. 54:157-162(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION AT ASN-45 AND ASN-271, PARTIAL PROTEIN SEQUENCE.
[7]"Ricin."
Olsnes S., Kozlov J.V.
Toxicon 39:1723-1728(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[8]"The three-dimensional structure of ricin at 2.8 A."
Monfort W., Villafranca J.E., Monzingo A.F., Ernst S.R., Katzin B., Rutenber E., Xuong N.H., Hamlin R., Robertus J.D.
J. Biol. Chem. 262:5398-5403(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
[9]"Structure of ricin A-chain at 2.5 A."
Katzin B.J., Collins E.J., Robertus J.D.
Proteins 10:251-259(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF A-CHAIN.
[10]"Structure of ricin B-chain at 2.5-A resolution."
Rutenber E., Robertus J.D.
Proteins 10:260-269(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF B-CHAIN.
[11]"X-ray structure of recombinant ricin A-chain at 1.8-A resolution."
Weston S.A., Tucker A.D., Thatcher D.R., Derbyshire D.J., Pauptit R.A.
J. Mol. Biol. 244:410-422(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF A-CHAIN.
[12]"Structure and activity of an active site substitution of ricin A chain."
Day P.J., Ernst S.R., Frankel A.E., Monzingo A.F., Pascal J.M., Molina-Svinth M.C., Robertus J.D.
Biochemistry 35:11098-11103(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF MUTANT HIS-215.
[13]"Structure-based identification of a ricin inhibitor."
Yan X., Hollis T., Svinth M., Day P., Monzingo A.F., Milne G.W., Robertus J.D.
J. Mol. Biol. 266:1043-1049(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF A-CHAIN.
[14]"Analysis of several key active site residues of ricin A chain by mutagenesis and X-ray crystallography."
Kin Y., Robertus J.D.
Protein Eng. 5:775-779(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS.
[15]"Genetic engineering of an immunotoxin to eliminate pulmonary vascular leak in mice."
Smallshaw J.E., Ghetie V., Rizo J., Fulmer J.R., Trahan L.L., Ghetie M.-A., Vitetta E.S.
Nat. Biotechnol. 21:387-391(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF ARG-83; LEU-109; ASP-110; VAL-111 AND ASN-132.
+Additional computationally mapped references.

Web resources

Protein Spotlight

Baneful beans - Issue 31 of February 2003

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X03179 Genomic DNA. Translation: CAA26939.1.
X52908 Genomic DNA. Translation: CAA37095.1.
X02388 mRNA. Translation: CAA26230.1.
PIRRLCSD. A24041.
RefSeqXP_002534649.1. XM_002534603.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
4MX1X-ray1.59A36-302[»]
4MX5X-ray1.52X36-302[»]
ProteinModelPortalP02879.
SMRP02879. Positions 36-302, 315-576.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid1022023. 1 interaction.
DIPDIP-46421N.
IntActP02879. 2 interactions.
MINTMINT-8391414.

Chemistry

BindingDBP02879.
ChEMBLCHEMBL4756.
DrugBankDB00173. Adenine.
DB00131. Adenosine monophosphate.

Protein family/group databases

Allergome2803. Ric c RIP.
CAZyCBM13. Carbohydrate-Binding Module Family 13.

PTM databases

UniCarbKBP02879.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID8287993.
KEGGrcu:RCOM_2159910.

Phylogenomic databases

ProtClustDBCLSN2726328.

Enzyme and pathway databases

BRENDA3.2.2.22. 1204.

Family and domain databases

Gene3D3.40.420.10. 1 hit.
4.10.470.10. 1 hit.
InterProIPR001574. Ribosome_inactivat_prot.
IPR017988. Ribosome_inactivat_prot_CS.
IPR016138. Ribosome_inactivat_prot_sub1.
IPR016139. Ribosome_inactivat_prot_sub2.
IPR017989. Ribosome_inactivat_prot_subgr.
IPR000772. Ricin_B_lectin.
[Graphical view]
PfamPF00652. Ricin_B_lectin. 2 hits.
PF00161. RIP. 1 hit.
[Graphical view]
PRINTSPR00396. SHIGARICIN.
SMARTSM00458. RICIN. 2 hits.
[Graphical view]
SUPFAMSSF50370. SSF50370. 2 hits.
SSF56371. SSF56371. 1 hit.
PROSITEPS50231. RICIN_B_LECTIN. 2 hits.
PS00275. SHIGA_RICIN. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP02879.

Entry information

Entry nameRICI_RICCO
AccessionPrimary (citable) accession number: P02879
Secondary accession number(s): P02880
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: August 13, 1987
Last modified: April 16, 2014
This is version 146 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Protein Spotlight

Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references