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(-) Description

Title :  CRYSTAL STRUCTURE OF RICIN A-CHAIN IN COMPLEX WITH THE CYCLIC TETRANUCLEOTIDE INHIBITOR, A TRANSITION STATE ANALOGUE
 
Authors :  M. Ho, M. B. Sturm, J. D. Goldman, S. C. Almo, V. L. Schramm
Date :  20 May 09  (Deposition) - 08 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Rta, Transition State, Ribosome Inactivating Proteins, Rips, Disulfide Bond, Glycoprotein, Hydrolase, Lectin, Nucleotide-Binding, Plant Defense, Protein Synthesis Inhibitor, Toxin, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Ho, M. B. Sturm, S. C. Almo, V. L. Schramm
Transition State Analogues In Structures Of Ricin And Saporin Ribosome-Inactivating Proteins.
Proc. Natl. Acad. Sci. Usa V. 106 20276 2009
PubMed-ID: 19920175  |  Reference-DOI: 10.1073/PNAS.0911606106

(-) Compounds

Molecule 1 - RICIN
    Chains: A
    EC Number: 3.2.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23A
    Expression System Strain: C43
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: CASTOR BEAN
    Organism Scientific: RICINUS COMMUNIS
    Organism Taxid: 3988
    Synonym: RICIN A CHAIN, RRNA N-GLYCOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1C2X1Ligand/Ion9,9'-{(2R,3R,3AR,5S,7AR,9R,10R,10AR,12S,23R,25AR,27R,28R,28AR,30S,32AR,35AR,37S,39AR)-9-(6-AMINO-9H-PURIN-9-YL)-34-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-5,12,23,30,37-PENTAHYDROXY-3,10,28-TRIMETHOXY-5,12,23,30,37-PENTAOXIDOTETRACOSAHYDRO-2H,7H,25H-TRIFURO[3,2-F:3',2'-L:3'',2''-X]PYRROLO[3,4-R][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]UNDECAOXAZAPENTAPHOSPHACYCLOPENTATRIACONTINE-2,27-DIYL}BIS(2-AMINO-3,9-DIHYDRO-6H-PURIN-6-ONE)
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:75 , ASN A:78 , ALA A:79 , TYR A:80 , VAL A:81 , PRO A:95 , ASP A:96 , ASP A:100 , GLY A:121 , TYR A:123 , ASP A:124 , ILE A:172 , GLU A:177 , ARG A:180 , ARG A:189 , THR A:190 , ARG A:193 , TYR A:194 , ASN A:209 , TRP A:211 , GLY A:212 , ARG A:213 , ARG A:258 , HOH A:321BINDING SITE FOR RESIDUE C2X A 268
2AC2SOFTWARETHR A:17 , HIS A:65 , HOH A:271BINDING SITE FOR RESIDUE SO4 A 269

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HIO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HIO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HIO)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RICI_RICCO207-223  1A:172-188

(-) Exons   (0, 0)

(no "Exon" information available for 3HIO)

(-) 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:259
 aligned with RICI_RICCO | P02879 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:259
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289         
           RICI_RICCO    40 QYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPP 298
               SCOP domains d3hioa_ A: Ricin A-chain                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3hioA01 A:5-179 Ricin (A subunit), domain 1                                                                                                                                    3hioA02 A:180-263 Ricin (A Subunit), domain 2                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhhhhhhh...eee..eee.......hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee....hhhhhhhhh.......eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee.hhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hio A   5 QYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPP 263
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (0, 0)

(no "Pfam Domain" information available for 3HIO)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RICI_RICCO | P02879)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
    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.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

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 Related Entries

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

UniProtKB/Swiss-Prot
        RICI_RICCO | P02879: 1br5 1br6 1ifs 1ift 1ifu 1il3 1il4 1il5 1il9 1j1m 1obs 1obt 1rtc 1uq4 1uq5 2aai 2p8n 2pjo 2r2x 2r3d 2vc3 2vc4 3bjg 3ej5 3lc9 3mk9 3px8 3px9 3rti 3rtj 3srp 4esi 4huo 4hup 4hv3 4hv7 4imv 4kuc 4lgp 4lgr 4lgs 4lhj 4lhq 4mx1 4mx5 4q2v 4z9k 5boz 5ddz 5e1h 5gu4 5j56 5j57 5sv3

(-) Related Entries Specified in the PDB File

3hiq 3his 3hit 3hiv 3hiw