VOLK_ADEVO
ID VOLK_ADEVO Reviewed; 523 AA.
AC Q70US9;
DT 22-APR-2020, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 72.
DE RecName: Full=Volkensin {ECO:0000303|PubMed:14686924, ECO:0000303|PubMed:16997573, ECO:0000303|PubMed:19591862, ECO:0000303|PubMed:3932357, ECO:0000312|EMBL:CAD61022.1};
DE AltName: Allergen=Ade v RIP {ECO:0000305};
DE Contains:
DE RecName: Full=Volkensin A chain {ECO:0000303|PubMed:14686924, ECO:0000303|PubMed:16997573, ECO:0000303|PubMed:3932357};
DE Short=VKA {ECO:0000303|PubMed:16997573};
DE EC=3.2.2.22 {ECO:0000269|PubMed:14686924, ECO:0000269|PubMed:16997573, ECO:0000269|PubMed:3932357};
DE AltName: Full=Ribosome-inactivating protein volkensin {ECO:0000303|PubMed:14686924, ECO:0000303|PubMed:16997573, ECO:0000303|PubMed:19591862};
DE Short=RIP VK {ECO:0000303|PubMed:14686924, ECO:0000303|PubMed:16997573};
DE AltName: Full=rRNA N-glycosidase {ECO:0000303|PubMed:14686924};
DE Contains:
DE RecName: Full=Volkensin B chain {ECO:0000303|PubMed:14686924, ECO:0000303|PubMed:16997573, ECO:0000303|PubMed:3932357};
DE Short=VKB {ECO:0000303|PubMed:16997573};
DE Flags: Fragment;
GN Name=volk38 {ECO:0000312|EMBL:CAD61022.1};
OS Adenia volkensii (Kilyambiti plant).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Malpighiales; Passifloraceae; Adenia.
OX NCBI_TaxID=219186 {ECO:0000312|EMBL:CAD61022.1};
RN [1] {ECO:0000312|EMBL:CAD61022.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-31; 23-38; 69-107;
RP 101-123; 105-117; 117-155; 118-139; 124-139; 127-137; 160-191; 168-174;
RP 185-205; 193-222; 206-235; 222-237; 238-250; 242-250; 266-285; 302-316;
RP 314-323; 353-368; 436-445; 445-460; 497-523 AND 506-523, FUNCTION
RP (VOLKENSIN A CHAIN), CATALYTIC ACTIVITY (VOLKENSIN A CHAIN), SUBUNIT,
RP TISSUE SPECIFICITY, MASS SPECTROMETRY (VOLKENSIN A CHAIN), AND 3D-STRUCTURE
RP MODELING.
RC TISSUE=Leaf {ECO:0000303|PubMed:14686924}, and
RC Root {ECO:0000303|PubMed:14686924};
RX PubMed=14686924; DOI=10.1046/j.1432-1033.2003.03909.x;
RA Chambery A., Di Maro A., Monti M.M., Stirpe F., Parente A.;
RT "Volkensin from Adenia volkensii Harms (kilyambiti plant), a type 2
RT ribosome-inactivating protein.";
RL Eur. J. Biochem. 271:108-117(2004).
RN [2]
RP PROTEIN SEQUENCE OF 1-7; 101-123; 127-137 AND 507-523, SUBUNIT, TISSUE
RP SPECIFICITY, AND 3D-STRUCTURE MODELING.
RC TISSUE=Root {ECO:0000269|PubMed:19591862};
RX PubMed=19591862; DOI=10.1016/j.ijbiomac.2009.06.015;
RA Severino V., Paiardini A., Pascarella S., Parente A., Chambery A.;
RT "Structural analysis of toxic volkensin, a type 2 ribosome inactivating
RT protein from Adenia volkensii Harm (kilyambiti plant): molecular modeling
RT and surface analysis by computational methods and limited proteolysis.";
RL Int. J. Biol. Macromol. 45:407-413(2009).
RN [3]
RP FUNCTION (VOLKENSIN A CHAIN AND VOLKENSIN B CHAIN), CATALYTIC ACTIVITY
RP (VOLKENSIN A CHAIN), ACTIVITY REGULATION (VOLKENSIN B CHAIN),
RP BIOPHYSICOCHEMICAL PROPERTIES (VOLKENSIN A CHAIN), SUBUNIT, TISSUE
RP SPECIFICITY, GLYCOSYLATION, AND TOXIC DOSE.
RX PubMed=3932357; DOI=10.1016/s0021-9258(17)38608-8;
RA Stirpe F., Barbieri L., Abbondanza A., Falasca A.I., Brown A.N.,
RA Sandvig K., Olsnes S., Pihl A.;
RT "Properties of volkensin, a toxic lectin from Adenia volkensii.";
RL J. Biol. Chem. 260:14589-14595(1985).
RN [4]
RP FUNCTION (VOLKENSIN A CHAIN).
RX PubMed=2930482; DOI=10.1042/bj2570723;
RA Brigotti M., Rambelli F., Zamboni M., Montanaro L., Sperti S.;
RT "Effect of alpha-sarcin and ribosome-inactivating proteins on the
RT interaction of elongation factors with ribosomes.";
RL Biochem. J. 257:723-727(1989).
RN [5]
RP ALLERGEN.
RX PubMed=16238796; DOI=10.1111/j.1365-2222.2005.02338.x;
RA Szalai K., Schoell I., Foerster-Waldl E., Polito L., Bolognesi A.,
RA Untersmayr E., Riemer A.B., Boltz-Nitulescu G., Stirpe F.,
RA Jensen-Jarolim E.;
RT "Occupational sensitization to ribosome-inactivating proteins in
RT researchers.";
RL Clin. Exp. Allergy 35:1354-1360(2005).
RN [6]
RP FUNCTION (VOLKENSIN A CHAIN AND VOLKENSIN B CHAIN), CATALYTIC ACTIVITY
RP (VOLKENSIN A CHAIN), SUBUNIT, AND TISSUE SPECIFICITY.
RX PubMed=16997573; DOI=10.1016/j.pep.2006.08.004;
RA Chambery A., Severino V., Stirpe F., Parente A.;
RT "Cloning and expression of the B chain of volkensin, type 2 ribosome
RT inactivating protein from Adenia volkensii harms: co-folding with the A
RT chain for heterodimer reconstitution.";
RL Protein Expr. Purif. 51:209-215(2007).
CC -!- FUNCTION: [Volkensin A chain]: Has N-glycosidase activity and is
CC responsible for inhibiting protein synthesis through the catalytic
CC inactivation of 60S ribosomal subunits by removing a specific adenine
CC of 28S rRNA (PubMed:14686924, PubMed:3932357, PubMed:2930482,
CC PubMed:16997573). Inhibits GTP-dependent binding of EF2 (elongation
CC factor 2) to ribosomes (PubMed:2930482). {ECO:0000269|PubMed:14686924,
CC ECO:0000269|PubMed:16997573, ECO:0000269|PubMed:2930482,
CC ECO:0000269|PubMed:3932357}.
CC -!- FUNCTION: [Volkensin B chain]: Binds to cell receptors and probably
CC facilitates the entry into the cell of the A chain (By similarity).
CC Acts also as a galactose-specific lectin responsible for cell
CC agglutination (PubMed:3932357, PubMed:16997573).
CC {ECO:0000250|UniProtKB:P81446, ECO:0000269|PubMed:16997573,
CC ECO:0000269|PubMed:3932357}.
CC -!- CATALYTIC ACTIVITY: [Volkensin A chain]:
CC Reaction=Endohydrolysis of the N-glycosidic bond at one specific
CC adenosine on the 28S rRNA.; EC=3.2.2.22; Evidence={ECO:0000255,
CC ECO:0000269|PubMed:14686924, ECO:0000269|PubMed:16997573,
CC ECO:0000269|PubMed:3932357};
CC -!- ACTIVITY REGULATION: [Volkensin B chain]: Hemagglutinating activity is
CC inhibited by galactose and structurally related sugars.
CC {ECO:0000269|PubMed:3932357}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES: [Volkensin A chain]:
CC Temperature dependence:
CC Loss of protein synthesis inhibiting activity of the rabbit
CC reticulocyte lysate by heating at 70 degrees Celsius for 20 minutes.
CC The inhibitory activity of the solution is almost completely lost
CC after storage for 2 weeks at 4 degrees Celsius in the presence of 1%
CC 2-mercaptoethanol. {ECO:0000269|PubMed:3932357};
CC -!- SUBUNIT: Disulfide-linked dimer of A and B chains.
CC {ECO:0000269|PubMed:14686924, ECO:0000269|PubMed:16997573,
CC ECO:0000269|PubMed:19591862, ECO:0000269|PubMed:3932357}.
CC -!- TISSUE SPECIFICITY: Expressed in roots (at protein level)
CC (PubMed:14686924, PubMed:3932357, PubMed:16997573, PubMed:19591862).
CC Expressed in seeds (at protein level) (PubMed:3932357).
CC {ECO:0000269|PubMed:14686924, ECO:0000269|PubMed:16997573,
CC ECO:0000269|PubMed:19591862, ECO:0000269|PubMed:3932357}.
CC -!- PTM: N-glycosylated. Contains mannose and galactose.
CC {ECO:0000269|PubMed:3932357}.
CC -!- MASS SPECTROMETRY: [Volkensin A chain]: Mass=28064;
CC Method=Electrospray; Note=The measured mass is that of the reduced
CC form.; Evidence={ECO:0000269|PubMed:14686924};
CC -!- ALLERGEN: Causes an allergic reaction in human. Natural protein was
CC found to bind to IgE of a patient who had been working with ribosome-
CC inactivating proteins for two years in a research laboratory setting.
CC {ECO:0000269|PubMed:16238796}.
CC -!- TOXIC DOSE: LD(50) is 0.32 ug/kg by intraperitoneal injection into rats
CC (at 48 hours post-injection). {ECO:0000269|PubMed:3932357}.
CC -!- TOXIC DOSE: LD(50) is 1.73 ug/kg by intraperitoneal injection into mice
CC (at 48 hours post-injection). {ECO:0000269|PubMed:3932357}.
CC -!- TOXIC DOSE: LD(50) is 0.061 ug/kg by intraperitoneal injection into
CC rats (at 14 days post-injection). {ECO:0000269|PubMed:3932357}.
CC -!- TOXIC DOSE: LD(50) is 1.38 ug/kg by intraperitoneal injection into mice
CC (at 14 days post-injection). {ECO:0000269|PubMed:3932357}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the ribosome-
CC inactivating protein family. Type 2 RIP subfamily. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AJ537497; CAD61022.1; -; Genomic_DNA.
DR AlphaFoldDB; Q70US9; -.
DR SMR; Q70US9; -.
DR Allergome; 2795; Ade v RIP.
DR CAZy; CBM13; Carbohydrate-Binding Module Family 13.
DR GO; GO:0030246; F:carbohydrate binding; IEA:UniProtKB-KW.
DR GO; GO:0030598; F:rRNA N-glycosylase activity; IEA:UniProtKB-EC.
DR GO; GO:0090729; F:toxin activity; IEA:UniProtKB-KW.
DR GO; GO:0006952; P:defense response; IEA:UniProtKB-KW.
DR GO; GO:0008152; P:metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0017148; P:negative regulation of translation; IEA:UniProtKB-KW.
DR CDD; cd00161; RICIN; 2.
DR Gene3D; 3.40.420.10; -; 1.
DR Gene3D; 4.10.470.10; -; 1.
DR InterPro; IPR036041; Ribosome-inact_prot_sf.
DR InterPro; IPR017989; Ribosome_inactivat_1/2.
DR InterPro; IPR001574; Ribosome_inactivat_prot.
DR InterPro; IPR017988; Ribosome_inactivat_prot_CS.
DR InterPro; IPR016138; Ribosome_inactivat_prot_sub1.
DR InterPro; IPR016139; Ribosome_inactivat_prot_sub2.
DR InterPro; IPR035992; Ricin_B-like_lectins.
DR InterPro; IPR000772; Ricin_B_lectin.
DR PANTHER; PTHR33453; PTHR33453; 1.
DR Pfam; PF00652; Ricin_B_lectin; 2.
DR Pfam; PF00161; RIP; 1.
DR PRINTS; PR00396; SHIGARICIN.
DR SMART; SM00458; RICIN; 2.
DR SUPFAM; SSF50370; SSF50370; 2.
DR SUPFAM; SSF56371; SSF56371; 1.
DR PROSITE; PS50231; RICIN_B_LECTIN; 2.
DR PROSITE; PS00275; SHIGA_RICIN; 1.
PE 1: Evidence at protein level;
KW Allergen; Direct protein sequencing; Disulfide bond; Glycoprotein;
KW Glycosidase; Hydrolase; Lectin; Plant defense; Protein synthesis inhibitor;
KW Toxin.
FT CHAIN <1..250
FT /note="Volkensin A chain"
FT /evidence="ECO:0000305|PubMed:14686924"
FT /id="PRO_0000449524"
FT PROPEP 251..265
FT /note="Linker peptide"
FT /evidence="ECO:0000305|PubMed:14686924"
FT /id="PRO_0000449525"
FT CHAIN 266..>523
FT /note="Volkensin B chain"
FT /evidence="ECO:0000305|PubMed:14686924"
FT /id="PRO_0000449526"
FT DOMAIN 270..397
FT /note="Ricin B-type lectin 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT DOMAIN 400..523
FT /note="Ricin B-type lectin 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT ACT_SITE 74
FT /evidence="ECO:0000250|UniProtKB:P84531"
FT ACT_SITE 113
FT /evidence="ECO:0000250|UniProtKB:P84531"
FT ACT_SITE 162
FT /evidence="ECO:0000250|UniProtKB:P84531"
FT ACT_SITE 165
FT /evidence="ECO:0000250|UniProtKB:P84531"
FT BINDING 111..113
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000250|UniProtKB:P02879"
FT BINDING 287..291
FT /ligand="a carbohydrate"
FT /ligand_id="ChEBI:CHEBI:16646"
FT /evidence="ECO:0000250|UniProtKB:P06750"
FT BINDING 300
FT /ligand="a carbohydrate"
FT /ligand_id="ChEBI:CHEBI:16646"
FT /evidence="ECO:0000250|UniProtKB:P06750"
FT BINDING 305
FT /ligand="a carbohydrate"
FT /ligand_id="ChEBI:CHEBI:16646"
FT /evidence="ECO:0000250|UniProtKB:P06750"
FT BINDING 311
FT /ligand="a carbohydrate"
FT /ligand_id="ChEBI:CHEBI:16646"
FT /evidence="ECO:0000250|UniProtKB:P06750"
FT BINDING 358
FT /ligand="a carbohydrate"
FT /ligand_id="ChEBI:CHEBI:16646"
FT /evidence="ECO:0000250|UniProtKB:P06750"
FT BINDING 398
FT /ligand="a carbohydrate"
FT /ligand_id="ChEBI:CHEBI:16646"
FT /evidence="ECO:0000250|UniProtKB:P06750"
FT CARBOHYD 358
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 398
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT DISULFID 245..269
FT /note="Interchain (between A and B chains)"
FT /evidence="ECO:0000250|UniProtKB:P06750"
FT DISULFID 285..304
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT DISULFID 328..343
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT DISULFID 414..427
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT DISULFID 453..471
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT CONFLICT 105
FT /note="R -> H (in Ref. 1; AA sequence and 2; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 118
FT /note="N -> H (in Ref. 1; AA sequence and 2; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 131
FT /note="V -> I (in Ref. 1; AA sequence and 2; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 180
FT /note="P -> L (in Ref. 1; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 182
FT /note="D -> E (in Ref. 1; AA sequence)"
FT /evidence="ECO:0000305"
FT NON_TER 1
FT /evidence="ECO:0000312|EMBL:CAD61022.1"
FT NON_TER 523
FT /evidence="ECO:0000312|EMBL:CAD61022.1"
SQ SEQUENCE 523 AA; 58251 MW; BBC5FE5B7F07D81A CRC64;
VFPKVPFDVP KATVESYTRF IRVLRDELAG GVSPQGIRRL RNPAEIQPSQ GFILIQLTGY
VGSVTLIMDV RNAYLLGYLS HNVLYHFNDV SASSIASVFP DAQRRQLPFG GGYPSMRNYA
PERDQIDHGI VELAYAVDRL YYSQNNNQIA LGLVICAGMV AEASRFRYIE GLVRQSIVGP
GDYRTFRPDA LMYSIVTQWQ TLSERIQGSF NGAFQPVQLG YASDPFYWDN VAQAITRLSL
MLFVCSQPPR QSDSPLVIRS FVDRNDPVCP SGETTAFIVG RDGRCVDVKV EEFFDGNKVQ
MWPCKSSQNA NQLWTLKRDG TIRCQGKCLT VRSPQLYAMI WDCTTFYAPA TKWEVWDNGT
IINPASGRVL TAPTGEAGVT LNLQFNEYAA SQAWRVTNVT VPTVTTIVGY DDLCLETNGN
GVWLANCVKG KAQQRWTLYA DGTIRSQSTL SKCLACSGSC VKLAKIVNTD CAGSANSRWY
FDNYGGIVNL RTGMVMDVKE SNPSLNEIIA HPWHGNSNQQ WFL
