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(-) Description

Title :  STUDIES ON CRYSTAL STRUCTURES ACTIVE CENTER GEOMETRY AND DEPURINE MECHANISM OF TWO RIBOSOME-INACTIVATING PROTEINS
 
Authors :  Q. Huang, S. Liu, Y. Tang, S. Jin, Y. Wang
Date :  01 Jul 94  (Deposition) - 07 Feb 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Ribosome-Inactivating Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Huang, S. Liu, Y. Tang, S. Jin, Y. Wang
Studies On Crystal Structures, Active-Centre Geometry And Depurinating Mechanism Of Two Ribosome-Inactivating Proteins.
Biochem. J. V. 309 285 1995
PubMed-ID: 7619070
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-TRICHOSANTHIN
    Chains: A
    Engineered: YES
    Organism Scientific: TRICHOSANTHES KIRILOWII
    Organism Taxid: 3677

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:69 , TYR A:70 , ILE A:71 , GLY A:109 , TYR A:111 , ILE A:155 , SER A:159 , GLU A:160 , ARG A:163 , HOH A:383BINDING SITE FOR RESIDUE ADN A 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIPT_TRIKI178-194  1A:155-171

(-) Exons   (0, 0)

(no "Exon" information available for 1MRJ)

(-) 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 RIPT_TRIKI | P09989 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:247
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       
           RIPT_TRIKI    24 DVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA 270
               SCOP domains d1mrja_ A: alpha-Trichosanthin                                                                                                                                                                                                                          SCOP domains
               CATH domains 1mrjA01 A:1-162 Ricin (A subunit), domain 1                                                                                                                       1mrjA02 A:163-247 Ricin (A Subunit), domain 2                                         CATH domains
               Pfam domains --RIP-1mrjA01 A:3-202                                                                                                                                                                                     --------------------------------------------- Pfam domains
     Sec.struct. author (1) eeeee....hhhhhhhhhhhhhhhh.....................eeeeeee...eeeeeeeeee...eeeeeee..------hhhhhhhhhh......eeeeeeeeeehhhhhhhhh....----hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhh......eeeeeeee.......eeeeeeehhhhhhh........... Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------------eeeeeee--------------------------------------eeeee----------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ---------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mrj A   1 DVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RIP] (62)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIPT_TRIKI | P09989)
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: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.
    GO:0050688    regulation of defense response to virus    Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RIPT_TRIKI | P09989: 1gis 1giu 1j4g 1mrk 1nli 1qd2 1tcs 2jdl 2jjr 2vs6

(-) Related Entries Specified in the PDB File

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