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Reviewed, UniProtKB/Swiss-Prot P33183 (NIGB_SAMNI)

Last modified June 16, 2009. Version 70. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    Nigrin b
Alternative name(s):
    Agglutinin V
    SNAV
Cleaved into the following 2 chains:
    1- Recommended name:
            Nigrin b A chain
              EC=3.2.2.22
        Alternative name(s):
            rRNA N-glycosidase
    2- Recommended name:
            Nigrin b B chain
OrganismSambucus nigra (European elder)
Taxonomic identifier4202 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › asterids › campanulids › Dipsacales › Adoxaceae › Sambucus

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Protein attributes

Sequence length563 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level.

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General annotation (Comments)

Function

Non-toxic type 2 RIP which strongly inhibits mammalian protein synthesis but does not affect plant nor bacterial protein synthesis. The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA.

The B chain is a galactose-specific lectin that facilitates the binding of nigrin b to the cell membrane that precedes endocytosis.

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.

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.

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2525 Ref.2
Chain26 – 297272Nigrin b A chain
PRO_0000030744
Chain298 – 563266Nigrin b B chain
PRO_0000030745

Regions

Domain305 – 431127Ricin B-type lectin 1
Repeat316 – 356411-alpha
Repeat357 – 397411-beta
Repeat400 – 432331-gamma
Domain434 – 559126Ricin B-type lectin 2
Repeat445 – 482382-alpha
Repeat486 – 524392-beta
Repeat527 – 554282-gamma

Sites

Active site1881 By similarity

Amino acid modifications

Glycosylation2211N-linked (GlcNAc...) Potential
Glycosylation3681N-linked (GlcNAc...) Potential
Glycosylation3761N-linked (GlcNAc...) Potential
Glycosylation4831N-linked (GlcNAc...) Potential
Glycosylation5371N-linked (GlcNAc...) Potential
Disulfide bond274 ↔ 302Interchain (between B and A chains) By similarity
Disulfide bond319 ↔ 338 By similarity
Disulfide bond360 ↔ 377 By similarity
Disulfide bond448 ↔ 463 By similarity
Disulfide bond489 ↔ 506 By similarity

Experimental info

Sequence conflict391K → V AA sequence Ref.2

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Sequences

Sequence LengthMass (Da)Tools
P33183-1 [UniParc].

Last modified December 5, 2001. Version 2.
Checksum: F250CBE24621BF14

FASTA56362,300
        10         20         30         40         50         60 
MRVVAAAMLY FYIVVLAICS VGIQGIDYPS VSFNLDGAKS ATYRDFLSNL RKTVATGTYE 

        70         80         90        100        110        120 
VNGLPVLRRE SEVQVKSRFV LVPLTNYNGN TVTLAVDVTN LYVVAFSGNA NSYFFKDATE 

       130        140        150        160        170        180 
VQKSNLFVGT KQNTLSFTGN YDNLETAANT RRESIELGPS PLDGAITSLY HGDSVARSLL 

       190        200        210        220        230        240 
VVIQMVSEAA RFRYIEQEVR RSLQQATSFT PNALMLSMEN NWSSMSLEIQ QAGNNVSPFF 

       250        260        270        280        290        300 
GTVQLLNYDH THRLVDNFEE LYKITGIAIL LFRCSSPSND NAIRMPLDLA GEDNKYNDGE 

       310        320        330        340        350        360 
TCTLRTSFTR NIVGRDGLCV DVRNGYDTDG TPLQLWPCGT QRNQRWTFDS DDTIRSMGKC 

       370        380        390        400        410        420 
MTANGLNNGS NIVIFNCSTA AENAIKWEVP IDGSIINPSS GLVMTAPRAA SRTILLLEDN 

       430        440        450        460        470        480 
IYAASQGWTV TNNVKPIVAS IVGYKEMCLQ SNGENNGVWM EDCEATSLQQ QWALYGDRTI 

       490        500        510        520        530        540 
RVNSTRGLCV TTNGYNSKDL IIILKCQGLP SQRWFFNSDG AIVNPKSRHV MDVRASNVSL 

       550        560 
REIIIFPATG NPNQQWVTQV LPS

« Hide

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References

[1]"Characterization and molecular cloning of Sambucus nigra agglutinin V (nigrin b), a GalNAc-specific type-2 ribosome-inactivating protein from the bark of elderberry (Sambucus nigra)."
Van Damme E.J., Barre A., Rouge P., Van Leuven F., Peumans W.J.
Eur. J. Biochem. 237:505-513(1996) [PubMed: 8647092] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Tissue: Bark.
[2]"Isolation and partial characterization of nigrin b, a non-toxic novel type 2 ribosome-inactivating protein from the bark of Sambucus nigra L."
Girbes T., Citores L., Ferreras J.M., Rojo M.A., Iglesias R., Munoz R., Arias F.J., Calonge M., Garcia J.R., Mendez E.
Plant Mol. Biol. 22:1181-1186(1993) [PubMed: 8400135] [Abstract]
Cited for: PROTEIN SEQUENCE OF 26-49 AND 298-321.
Tissue: Bark.
+Additional computationally mapped references.

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Cross-references

Sequence databases

U41299 mRNA. Translation: AAB39475.1.
PIRS37382.
S37383.

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
3C9ZX-ray1.35A306-563[»]
3CA0X-ray1.95A306-563[»]
3CA1X-ray1.55A306-563[»]
3CA3X-ray1.55A306-563[»]
3CA4X-ray1.55A306-563[»]
3CA5X-ray1.55A306-563[»]
3CA6X-ray1.40A306-563[»]
3CAHX-ray1.55A306-563[»]
SMRP33183. Positions 26-274, 299-560.
ModBaseSearch...

Enzyme and pathway databases

BRENDA3.2.2.22. 273569.

Family and domain databases

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]
Gene3DG3DSA:3.40.420.10. Ribosome_inactivat_prot_sub1. 1 hit.
G3DSA:4.10.470.10. Ribosome_inactivat_prot_sub2. 1 hit.
PfamPF00652. Ricin_B_lectin. 2 hits.
PF00161. RIP. 1 hit.
[Graphical view]
PRINTSPR00396. SHIGARICIN.
SMARTSM00458. RICIN. 2 hits.
[Graphical view]
PROSITEPS50231. RICIN_B_LECTIN. 2 hits.
PS00275. SHIGA_RICIN. 1 hit.
[Graphical view]
ProtoNetSearch...

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Entry information

Entry nameNIGB_SAMNI
AccessionPrimary (citable) accession number: P33183
Secondary accession number(s): P33184, P93542
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: December 5, 2001
Last modified: June 16, 2009
This is version 70 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectPPAP (Plant Proteome Annotation Project)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents