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(-) Description

Title :  ATOMIC RESOLUTION STRUCTURE OF CUCURMOSIN, A NOVEL TYPE 1 RIP FROM THE SARCOCARP OF CUCURBITA MOSCHATA
 
Authors :  L. Chen
Date :  09 Jan 08  (Deposition) - 07 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Rip Fold, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Hou, E. J. Meehan, J. Xie, M. Huang, M. Chen, L. Chen
Atomic Resolution Structure Of Cucurmosin, A Novel Type 1 Ribosome-Inactivating Protein From The Sarcocarp Of Cucurbita Moschata.
J. Struct. Biol. V. 164 81 2008
PubMed-ID: 18652900  |  Reference-DOI: 10.1016/J.JSB.2008.06.011

(-) Compounds

Molecule 1 - CUCURMOSIN
    Chains: A
    Organism Scientific: CUCURBITA MOSCHATA
    Other Details: SARCOCARP OF PUMPKIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 12)

Asymmetric/Biological Unit (6, 12)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PO41Ligand/IonPHOSPHATE ION
6XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:206 , ASN A:225 , THR A:227 , SER A:228 , NAG A:247 , PO4 A:252 , HOH A:289 , HOH A:334 , HOH A:478BINDING SITE FOR RESIDUE NAG A 246
02AC2SOFTWARENAG A:246 , BMA A:248 , XYP A:251 , HOH A:453 , HOH A:500BINDING SITE FOR RESIDUE NAG A 247
03AC3SOFTWARENAG A:247 , MAN A:249 , MAN A:250 , XYP A:251 , HOH A:500BINDING SITE FOR RESIDUE BMA A 248
04AC4SOFTWAREASP A:56 , ASN A:219 , ARG A:220 , BMA A:248 , XYP A:251 , HOH A:326 , HOH A:332 , HOH A:352 , HOH A:448 , HOH A:465BINDING SITE FOR RESIDUE MAN A 249
05AC5SOFTWAREASN A:1 , VAL A:2 , ARG A:3 , HIS A:139 , BMA A:248 , HOH A:422 , HOH A:501BINDING SITE FOR RESIDUE MAN A 250
06AC6SOFTWAREASP A:215 , NAG A:247 , BMA A:248 , MAN A:249 , HOH A:457 , HOH A:459 , HOH A:500BINDING SITE FOR RESIDUE XYP A 251
07AC7SOFTWARESER A:228 , ASN A:229 , NAG A:246 , HOH A:315 , HOH A:457 , HOH A:459BINDING SITE FOR RESIDUE PO4 A 252
08AC8SOFTWAREGLY A:107 , ARG A:161 , HOH A:276 , HOH A:402BINDING SITE FOR RESIDUE EDO A 253
09AC9SOFTWARESER A:59 , ILE A:60 , THR A:61BINDING SITE FOR RESIDUE EDO A 254
10BC1SOFTWAREASP A:33 , THR A:232 , GLN A:236 , HOH A:271 , HOH A:449BINDING SITE FOR RESIDUE EDO A 255
11BC2SOFTWARETYR A:164 , LEU A:167 , GLN A:233 , ASN A:234BINDING SITE FOR RESIDUE EDO A 256
12BC3SOFTWARELYS A:27 , LYS A:30 , HOH A:416BINDING SITE FOR RESIDUE EDO A 257

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIP_CUCMO153-169  1A:153-169

(-) Exons   (0, 0)

(no "Exon" information available for 3BWH)

(-) 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:244
 aligned with D0VWS7_CUCMO | D0VWS7 from UniProtKB/TrEMBL  Length:245

    Alignment length:244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
         D0VWS7_CUCMO     1 NVRFDLSSATSSSYKTFIKNLREALPKDGKVYDIPVLLSTVMDSRRFILIDLVNYDGQSITAAIDVLNVYIVAYSTGTVSYFFQQVPAQAPKLLFKGTQQRTLPYTGNYENLQTAAKKLRENIELGLPALDSAITTLFHYNAEAAASALLVLIQTTSEAARFRYIELQIANNVGTKFKPSQTIISLENNWSALSKQIQIAKNKNGQFETPVILIDPQGNRVQITNVTSNVVTQNIQLLLNIGAT 244
               SCOP domains d3bwha_ A: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 3bwhA01 A:1-160 Ricin (A subunit), domain 1                                                                                                                     3bwhA02 A:161-244 Ricin (A Subunit), domain 2                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhhhhh.eeeee..eeee....hhhh.eeeeeee.....eeeeeee.....eeeee...eeee......hhhhhh....eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhh......hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bwh A   1 NVRFDLSSATSSSYKTFIKNLREALPKDGKVYDIPVLLSTVMDSRRFILIDLVNYDGQSITAAIDVLNVYIVAYSTGTVSYFFQQVPAQAPKLLFKGTQQRTLPYTGNYENLQTAAKKLRENIELGLPALDSAITTLFHYNAEAAASALLVLIQTTSEAARFRYIELQIANNVGTKFKPSQTIISLENNWSALSKQIQIAKNKNGQFETPVILIDPQGNRVQITNVTSNVVTQNIQLLLNIGAT 244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    


Chain A from PDB  Type:PROTEIN  Length:244
 aligned with RIP_CUCMO | P84531 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
            RIP_CUCMO     1 NVRFDLSSATSSSYKTFIKNLREALPKDGKVYDIPVLLSTVMDSRRFILIDLVNYDGQSITAAIDVLNVYIVAYSTGTVSYFFQQVPAQAPKLLFKGTQQRTLPYTGNYENLQTAAKKLRENIELGLPALDSAITTLFHYNAEAAASALLVLIQTTSEAARFRYIELQIANNVGTKFKPSQTIISLENNWSALSKQIQIAKNKNGQFETPVILIDPQGNRVQITNVTSNVVTQNIQLLLNIGAT 244
               SCOP domains d3bwha_ A: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 3bwhA01 A:1-160 Ricin (A subunit), domain 1                                                                                                                     3bwhA02 A:161-244 Ricin (A Subunit), domain 2                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhhhhh.eeeee..eeee....hhhh.eeeeeee.....eeeeeee.....eeeee...eeee......hhhhhh....eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhh......hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bwh A   1 NVRFDLSSATSSSYKTFIKNLREALPKDGKVYDIPVLLSTVMDSRRFILIDLVNYDGQSITAAIDVLNVYIVAYSTGTVSYFFQQVPAQAPKLLFKGTQQRTLPYTGNYENLQTAAKKLRENIELGLPALDSAITTLFHYNAEAAASALLVLIQTTSEAARFRYIELQIANNVGTKFKPSQTIISLENNWSALSKQIQIAKNKNGQFETPVILIDPQGNRVQITNVTSNVVTQNIQLLLNIGAT 244
                                    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)
  - → 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 3BWH)

(-) Gene Ontology  (4, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D0VWS7_CUCMO | D0VWS7)
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.

Chain A   (RIP_CUCMO | P84531)
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.

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 Related Entries

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