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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-LUFFIN, A RIBOSOME INACTIVATING PROTEIN AT 2.0A RESOLUTION
 
Authors :  S. Wu
Date :  24 Dec 02  (Deposition) - 05 Aug 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Ribosome Inactivating Protein(Rip), Beta-Luffin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. J. Ma, J. H. Li, H. G. Li, S. Wu, Y. C. Dong
Crystal Structure Of Beta-Luffin, A Ribosome-Inactivating Protein, At 2. 0 A Resolution.
Acta Crystallogr. , Sect. D V. 59 1366 2003
PubMed-ID: 12876337  |  Reference-DOI: 10.1107/S0907444903011156

(-) Compounds

Molecule 1 - B-LUFFIN
    Chains: A
    EC Number: 3.2.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1-247
    Organism Common: SMOOTH LOOFAH
    Organism Scientific: LUFFA AEGYPTIACA
    Organism Taxid: 3670
    Synonym: BETA-LUFFIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:2 , ALA A:25 , ASN A:235BINDING SITE FOR RESIDUE NAG A 248
2AC2SOFTWAREASN A:78 , TYR A:82 , PHE A:140 , HIS A:141 , TYR A:142 , HOH A:319BINDING SITE FOR RESIDUE NAG A 249
3AC3SOFTWARESER A:43 , ASN A:85 , THR A:104 , LEU A:105BINDING SITE FOR RESIDUE NAG A 250

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NIO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NIO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NIO)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIPB_LUFAE155-171  1A:156-171

(-) Exons   (0, 0)

(no "Exon" information available for 1NIO)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:247
 aligned with RIPB_LUFAE | P22851 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
           RIPB_LUFAE     1 ANVSFSLSGADSKSYSKFITALRKALPSKEKVSNIPLLLPSASGASRYILMQLSNYDAKAITMAIDVTNVYIMGYLVNSTSYFANESDAKLASQYVFKGSTLVTIPYSGNYERLQNAAGKIREKIPLGFRALDSALTSIFHYDSTAAAAAFLVILQTTAEASRFKYIEGQIIERIPKNEVPSPAALSLENEAWSLLSKQIQLAQTNNGAFRTPVVIIDNKGQRVEITNLASKVQIKDVNSKLLLNKQNIA 250
               SCOP domains d1nioa_ A: Beta-luffin                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1nioA01 A:1-162 Ricin (A subunit), domain 1                                                                                                                       1nioA02 A:163-247 Ricin (A Su bunit), domain 2                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhhhh.eeeee..eeee....hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh.......eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh-hhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhh--......hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nio A   1 ANVSFSLSGADSKSYSKFITALRKALPSKEKVSNIPLLLPSASGASRYILMQLSNYDAKAITMAIDVTNVYIMGYLVNSTSYFFNESDAKLASQYVFKGSTIVTLPYSGNYERLQNAAGKVREKIPLGFRAFDSAITSLFHYDSTAAAGAFLVIIQTTAEASRFKYIEGQIIKRIPKNEVPSPAALSLENE-WSALSKQIQLAQTNNGAFRTPVVIIDNKGQRVEIKDVNSKVVTN--NIKLLLNKQNIA 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190| |    199       209       219       229     | 237       247
                                                                                                                                                                                                                        191 |                                        235  |           
                                                                                                                                                                                                                          192                                           236
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NIO)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIPB_LUFAE | P22851)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0030598    rRNA N-glycosylase activity    Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

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