NIGB_SAMNI
ID NIGB_SAMNI Reviewed; 563 AA.
AC P33183; P33184; P93542;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 05-DEC-2001, sequence version 2.
DT 25-MAY-2022, entry version 107.
DE RecName: Full=Nigrin b;
DE AltName: Full=Agglutinin V;
DE AltName: Full=SNAV;
DE Contains:
DE RecName: Full=Nigrin b A chain;
DE EC=3.2.2.22;
DE AltName: Full=rRNA N-glycosidase;
DE Contains:
DE RecName: Full=Nigrin b B chain;
DE Flags: Precursor;
OS Sambucus nigra (European elder).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC asterids; campanulids; Dipsacales; Adoxaceae; Sambucus.
OX NCBI_TaxID=4202;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Bark;
RX PubMed=8647092; DOI=10.1111/j.1432-1033.1996.0505k.x;
RA Van Damme E.J., Barre A., Rouge P., Van Leuven F., Peumans W.J.;
RT "Characterization and molecular cloning of Sambucus nigra agglutinin V
RT (nigrin b), a GalNAc-specific type-2 ribosome-inactivating protein from the
RT bark of elderberry (Sambucus nigra).";
RL Eur. J. Biochem. 237:505-513(1996).
RN [2]
RP PROTEIN SEQUENCE OF 26-49 AND 298-321.
RC TISSUE=Bark;
RX PubMed=8400135; DOI=10.1007/bf00028990;
RA Girbes T., Citores L., Ferreras J.M., Rojo M.A., Iglesias R., Munoz R.,
RA Arias F.J., Calonge M., Garcia J.R., Mendez E.;
RT "Isolation and partial characterization of nigrin b, a non-toxic novel type
RT 2 ribosome-inactivating protein from the bark of Sambucus nigra L.";
RL Plant Mol. Biol. 22:1181-1186(1993).
CC -!- FUNCTION: Non-toxic type 2 RIP which strongly inhibits mammalian
CC protein synthesis but does not affect plant nor bacterial protein
CC synthesis. The A chain is responsible for inhibiting protein synthesis
CC through the catalytic inactivation of 60S ribosomal subunits by
CC removing adenine from position 4,324 of 28S rRNA.
CC -!- FUNCTION: The B chain is a galactose-specific lectin that facilitates
CC the binding of nigrin b to the cell membrane that precedes endocytosis.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endohydrolysis of the N-glycosidic bond at one specific
CC adenosine on the 28S rRNA.; EC=3.2.2.22;
CC -!- SUBUNIT: Disulfide-linked dimer of A and B chains.
CC -!- SIMILARITY: In the N-terminal section; belongs to the ribosome-
CC inactivating protein family. Type 2 RIP subfamily. {ECO:0000305}.
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DR EMBL; U41299; AAB39475.1; -; mRNA.
DR PIR; S37382; S37382.
DR PIR; S37383; S37383.
DR PDB; 3C9Z; X-ray; 1.35 A; A=306-563.
DR PDB; 3CA0; X-ray; 1.95 A; A=306-563.
DR PDB; 3CA1; X-ray; 1.55 A; A=306-563.
DR PDB; 3CA3; X-ray; 1.55 A; A=306-563.
DR PDB; 3CA4; X-ray; 1.55 A; A=306-563.
DR PDB; 3CA5; X-ray; 1.55 A; A=306-563.
DR PDB; 3CA6; X-ray; 1.40 A; A=306-563.
DR PDB; 3CAH; X-ray; 1.55 A; A=306-563.
DR PDBsum; 3C9Z; -.
DR PDBsum; 3CA0; -.
DR PDBsum; 3CA1; -.
DR PDBsum; 3CA3; -.
DR PDBsum; 3CA4; -.
DR PDBsum; 3CA5; -.
DR PDBsum; 3CA6; -.
DR PDBsum; 3CAH; -.
DR AlphaFoldDB; P33183; -.
DR SMR; P33183; -.
DR UniLectin; P33183; -.
DR EvolutionaryTrace; P33183; -.
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: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; 2.
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 3D-structure; Direct protein sequencing; Disulfide bond; Glycoprotein;
KW Hydrolase; Lectin; Plant defense; Protein synthesis inhibitor; Repeat;
KW Signal; Toxin.
FT SIGNAL 1..25
FT /evidence="ECO:0000269|PubMed:8400135"
FT CHAIN 26..297
FT /note="Nigrin b A chain"
FT /id="PRO_0000030744"
FT CHAIN 298..563
FT /note="Nigrin b B chain"
FT /id="PRO_0000030745"
FT DOMAIN 305..431
FT /note="Ricin B-type lectin 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT REPEAT 316..356
FT /note="1-alpha"
FT REPEAT 357..397
FT /note="1-beta"
FT REPEAT 400..432
FT /note="1-gamma"
FT DOMAIN 434..559
FT /note="Ricin B-type lectin 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT REPEAT 445..482
FT /note="2-alpha"
FT REPEAT 486..524
FT /note="2-beta"
FT REPEAT 527..554
FT /note="2-gamma"
FT ACT_SITE 188
FT /evidence="ECO:0000250"
FT CARBOHYD 221
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 368
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 376
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 483
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 537
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 274..302
FT /note="Interchain (between B and A chains)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT DISULFID 319..338
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT DISULFID 360..377
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT DISULFID 448..463
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT DISULFID 489..506
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00174"
FT CONFLICT 39
FT /note="K -> V (in Ref. 2; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 308..313
FT /evidence="ECO:0007829|PDB:3C9Z"
FT HELIX 315..317
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 319..322
FT /evidence="ECO:0007829|PDB:3C9Z"
FT HELIX 323..325
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 332..336
FT /evidence="ECO:0007829|PDB:3C9Z"
FT HELIX 342..344
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 346..348
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 354..356
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 359..367
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 371..375
FT /evidence="ECO:0007829|PDB:3C9Z"
FT TURN 377..379
FT /evidence="ECO:0007829|PDB:3C9Z"
FT HELIX 382..384
FT /evidence="ECO:0007829|PDB:3C9Z"
FT TURN 398..400
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 403..405
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 407..410
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 416..418
FT /evidence="ECO:0007829|PDB:3C9Z"
FT HELIX 424..426
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 429..432
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 437..442
FT /evidence="ECO:0007829|PDB:3C9Z"
FT HELIX 444..446
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 448..450
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 459..461
FT /evidence="ECO:0007829|PDB:3C9Z"
FT HELIX 468..470
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 472..474
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 480..482
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 485..496
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 500..505
FT /evidence="ECO:0007829|PDB:3C9Z"
FT HELIX 510..512
FT /evidence="ECO:0007829|PDB:3C9Z"
FT TURN 525..527
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 530..533
FT /evidence="ECO:0007829|PDB:3C9Z"
FT HELIX 534..536
FT /evidence="ECO:0007829|PDB:3C9Z"
FT HELIX 538..540
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 543..546
FT /evidence="ECO:0007829|PDB:3C9Z"
FT HELIX 552..554
FT /evidence="ECO:0007829|PDB:3C9Z"
FT STRAND 557..560
FT /evidence="ECO:0007829|PDB:3C9Z"
SQ SEQUENCE 563 AA; 62300 MW; F250CBE24621BF14 CRC64;
MRVVAAAMLY FYIVVLAICS VGIQGIDYPS VSFNLDGAKS ATYRDFLSNL RKTVATGTYE
VNGLPVLRRE SEVQVKSRFV LVPLTNYNGN TVTLAVDVTN LYVVAFSGNA NSYFFKDATE
VQKSNLFVGT KQNTLSFTGN YDNLETAANT RRESIELGPS PLDGAITSLY HGDSVARSLL
VVIQMVSEAA RFRYIEQEVR RSLQQATSFT PNALMLSMEN NWSSMSLEIQ QAGNNVSPFF
GTVQLLNYDH THRLVDNFEE LYKITGIAIL LFRCSSPSND NAIRMPLDLA GEDNKYNDGE
TCTLRTSFTR NIVGRDGLCV DVRNGYDTDG TPLQLWPCGT QRNQRWTFDS DDTIRSMGKC
MTANGLNNGS NIVIFNCSTA AENAIKWEVP IDGSIINPSS GLVMTAPRAA SRTILLLEDN
IYAASQGWTV TNNVKPIVAS IVGYKEMCLQ SNGENNGVWM EDCEATSLQQ QWALYGDRTI
RVNSTRGLCV TTNGYNSKDL IIILKCQGLP SQRWFFNSDG AIVNPKSRHV MDVRASNVSL
REIIIFPATG NPNQQWVTQV LPS
