Reviewed, UniProtKB/Swiss-Prot P93543 (RIP1_SAMNI)

Names and origin

Protein names	Recommended name:     Ribosome-inactivating protein SNAI' Cleaved into the following 3 chains:     1- Recommended name:             SNAI' A chain               EC=3.2.2.22         Alternative name(s):             rRNA N-glycosidase     2- Recommended name:             Linker peptide     3- Recommended name:             SNAI' B chain
Organism	Sambucus nigra (European elder)
Taxonomic identifier	4202 [NCBI]
Taxonomic lineage	Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › asterids › campanulids › Dipsacales › Adoxaceae › Sambucus

Protein attributes

Sequence length	569 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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 binds to cell receptors and probably facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (lectin activity). Agglutination is inhibited by Neu5Ac(alpha2,6)lactose, and N-linked glycoproteins such as fetuin and orosomucoid. Ref.1
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. Ref.1
Domain	The B chain is composed of two domains, each domain consists of 3 homologous subdomains (alpha, beta, gamma).
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.

Ontologies

Keywords
Biological process	Plant defense
Domain	Repeat Signal
Ligand	Lectin
Molecular function	Glycosidase Hydrolase Protein synthesis inhibitor Toxin
PTM	Disulfide bond Glycoprotein
Technical term	Direct protein sequencing
Gene Ontology (GO)
Biological process	defense response Inferred from electronic annotation. Source: UniProtKB-KW metabolic process Inferred from electronic annotation. Source: UniProtKB-KW negative regulation of translation Inferred from electronic annotation. Source: UniProtKB-KW pathogenesis Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	rRNA N-glycosylase activity Inferred from electronic annotation. Source: EC sugar binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Signal peptide	1 – 28	28	Ref.1
	Chain	29 – 291	263	SNAI' A chain		PRO_0000030746
	Peptide	292 – 303	12	Linker peptide		PRO_0000030747
	Chain	304 – 569	266	SNAI' B chain		PRO_0000030748
Regions
	Domain	315 – 435	121	Ricin B-type lectin 1
	Repeat	325 – 365	41	1-alpha
	Repeat	366 – 401	36	1-beta
	Repeat	404 – 436	33	1-gamma
	Domain	437 – 565	129	Ricin B-type lectin 2
	Repeat	448 – 488	41	2-alpha
	Repeat	492 – 530	39	2-beta
	Repeat	533 – 566	34	2-gamma
Sites
	Active site	201	1	By similarity
Amino acid modifications
	Glycosylation	40	1	N-linked (GlcNAc...) Potential
	Disulfide bond	286 ↔ 311		Interchain (between A and B chains) By similarity
	Disulfide bond	328 ↔ 347		By similarity
	Disulfide bond	369 ↔ 381		By similarity
	Disulfide bond	451 ↔ 466		By similarity
	Disulfide bond	495 ↔ 512		By similarity

Sequences

	Sequence		Length	Mass (Da)
	P93543-1 [UniParc]. Last modified May 1, 1997. Version 1. Checksum: 82B9C889A3E1F9AD	FASTA	569	62,598
	10 20 30 40 50 60 MKVVATILYL VVLAICGLGI HGAHPTHSAP PTVYPSVSFN LTEANSNEYR HFLQELRGKV 70 80 90 100 110 120 ILGSHRAFDL PVLNPESKVS DSDRFVLVRL TNPSRKKVTL AIDVVTFYVV AFAQNDRSYF 130 140 150 160 170 180 FSGSSEVQRE NLFVDTTQED LNFKGDYTSL EHQVGFGRVY IPLGPKSLAQ SISSLSTYKS 190 200 210 220 230 240 SAGDNKRLAR SLLVVIQMVS EAARFRYIQL RIQASITDAK EFTPDLLMLS MENKWSSMSS 250 260 270 280 290 300 EIQQAQPGGA FAQVVKLLDQ RNHPIDVTNF RRLFQLTSVA VLLHGCPTVT KMPAYIIKMP 310 320 330 340 350 360 VFNGGEDEER CSVVEEVTRR IGGRDGFCAE VKNGDEKDGT PVQLSSCGEQ SNQQWTFSTD 370 380 390 400 410 420 GTIQSLGKCL TTSSSVMIYN CKVVPPESTK WVVSIDGTIT NPRSGLVLTA PKAAEGTLVS 430 440 450 460 470 480 LEKNVHAARQ GWIVGNVEPL VTFIVGYEQM CLETNPGNND VSLGDCSVKS ASKVDQKWAL 490 500 510 520 530 540 YGDGTIRVNN DRSLCVTSEG KSSNEPIIIL KCLGWANQRW VFNTDGTISN PDSKLVMHVD 550 560 QNDVPLRKII LSHPSGTSNQ QWIASTHPA

References

[1]

"Elderberry (Sambucus nigra) bark contains two structurally different Neu5Ac(alpha2,6)Gal/GalNAc-binding type 2 ribosome-inactivating proteins." van Damme E.J.M., Roy S., Barre A., Citores L., Mostafapous K., Rouge P., Van Leuven F., Girbes T., Goldstein I.J., Peumans W.J. Eur. J. Biochem. 245:648-655(1997) [PubMed: 9183001] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 29-38 AND 304-309, FUNCTION, SUBUNIT. Tissue: Bark.

Cross-references

Sequence databases
EMBLGenBankDDBJ	U66191 mRNA. Translation: AAC49754.1.
3D structure databases
HSSP	HSSP built from PDB template 1HWM based on UniProtKB Q9AVR2.
ModBase	Search...
Enzyme and pathway databases
BRENDA	3.2.2.22. 273569.
Family and domain databases
InterPro	IPR001574. 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]
Gene3D	G3DSA:3.40.420.10. Ribosome_inactivat_prot_sub1. 1 hit. G3DSA:4.10.470.10. Ribosome_inactivat_prot_sub2. 1 hit.
Pfam	PF00652. Ricin_B_lectin. 2 hits. PF00161. RIP. 1 hit. [Graphical view]
PRINTS	PR00396. SHIGARICIN.
SMART	SM00458. RICIN. 2 hits. [Graphical view]
PROSITE	PS50231. RICIN_B_LECTIN. 2 hits. PS00275. SHIGA_RICIN. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RIP1_SAMNI

Accession

Primary (citable) accession number: P93543

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2004
Last sequence update:	May 1, 1997
Last modified:	June 16, 2009
This is version 50 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)