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(-) Description

Title :  CRYSTAL STRUCTURE OF INACTIVE RIBOSOME INACTIVATING PROTEIN FROM MAIZE (B-32)
 
Authors :  A. N. S. Mak, Y. T. Wong, J. A Young, S. S. Cha, K. H. Sze, S. W. N. Au, K. B. Wong, P. C. Shaw
Date :  02 May 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pro-Rip, Ribosome Inactivating Protein, Maize, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. N. Mak, Y. T. Wong, Y. J. An, S. S. Cha, K. H. Sze, S. W. Au, K. B. Wong, P. C. Shaw
Structure-Function Study Of Maize Ribosome-Inactivating Protein: Implications For The Internal Inactivation Region And The Sole Glutamate In The Active Site.
Nucleic Acids Res. V. 35 6259 2007
PubMed-ID: 17855394  |  Reference-DOI: 10.1093/NAR/GKM687
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOME-INACTIVATING PROTEIN 3
    ChainsA, B
    EC Number3.2.2.22
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System StrainC41
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCRIP3
    Organism ScientificZEA MAYS
    Organism Taxid4577
    SynonymRRNA N-GLYCOSIDASE, B-32 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2PQG)

(-) Sites  (0, 0)

(no "Site" information available for 2PQG)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PQG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PQG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PQG)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIP3_MAIZE202-218
 
  2A:202-218
B:202-218
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIP3_MAIZE202-218
 
  1A:202-218
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIP3_MAIZE202-218
 
  1-
B:202-218

(-) Exons   (0, 0)

(no "Exon" information available for 2PQG)

(-) Sequences/Alignments

Asymmetric 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:257
 aligned with RIP3_MAIZE | P25891 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:263
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281   
           RIP3_MAIZE    22 KFTEIFPVEDANYPYSAFIASVRKDVIKHCTDHKGIFQPVLPPEKKVPELWLYTELKTRTSSITLAIRMDNLYLVGFRTPGGVWWEFGKDGDTHLLGDNPRWLGFGGRYQDLIGNKGLETVTMGRAEMTRAVNDLAKKKKMATLEEEEVQMQMQMPEAADLAAAAAADPQADTKSKLVKLVVMVCEGLRFNTVSRTVDAGFNSQHGVTLTVTQGKQVQKWDRISKAAFEWADHPTAVIPDMQKLGIKDKNEAARIVALVKNQT 284
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhh......................eeeeeee....eeeeeee.....eeeee.....eee..............ee.....hhhhhh...hhhhh..hhhhhhhhhhhhh.............------..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh....hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pqg A  22 KFTEIFPVEDANYPYSAFIASVRKDVIKHCTDHKGIFQPVLPPEKKVPELWLYTELKTRTSSITLAIRMDNLYLVGFRTPGGVWWEFGKDGDTHLLGDNPRWLGFGGRYQDLIGNKGLETVTMGRAEMTRAVNDLAKKKKMATLEEEEV------PEAADLAAAAAADPQADTKSKLVKLVVMVCEGLRFNTVSRTVDAGFNSQHGVTLTVTQGKQVQKWDRISKAAFEWADHPTAVIPDMQKLGIKDKNEAARIVALVKNQT 284
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161        |-     | 181       191       201       211       221       231       241       251       261       271       281   
                                                                                                                                                                              170    177                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with RIP3_MAIZE | P25891 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:264
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281    
           RIP3_MAIZE    22 KFTEIFPVEDANYPYSAFIASVRKDVIKHCTDHKGIFQPVLPPEKKVPELWLYTELKTRTSSITLAIRMDNLYLVGFRTPGGVWWEFGKDGDTHLLGDNPRWLGFGGRYQDLIGNKGLETVTMGRAEMTRAVNDLAKKKKMATLEEEEVQMQMQMPEAADLAAAAAADPQADTKSKLVKLVVMVCEGLRFNTVSRTVDAGFNSQHGVTLTVTQGKQVQKWDRISKAAFEWADHPTAVIPDMQKLGIKDKNEAARIVALVKNQTT 285
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----RIP-2pqgB01 B:26-251                                                                                                                                                                                                              ---------------------------------- Pfam domains (1)
           Pfam domains (2) ----RIP-2pqgB02 B:26-251                                                                                                                                                                                                              ---------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhh.eee..eeeee..........eeeeeee....eeeeeee.....eeeee.....eee..............ee.....hhhhhhh..hhhhh..hhhhhhhhhhhhh...........-----------...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh....hhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pqg B  22 KFTEIFPVEDANYPYSAFIASVRKDVIKHCTDHKGIFQPVLPPEKKVPELWLYTELKTRTSSITLAIRMDNLYLVGFRTPGGVWWEFGKDGDTHLLGDNPRWLGFGGRYQDLIGNKGLETVTMGRAEMTRAVNDLAKKKKMATLEEE-----------ADLAAAAAADPQADTKSKLVKLVVMVCEGLRFNTVSRTVDAGFNSQHGVTLTVTQGKQVQKWDRISKAAFEWADHPTAVIPDMQKLGIKDKNEAARIVALVKNQTT 285
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161      |  -       181       191       201       211       221       231       241       251       261       271       281    
                                                                                                                                                                            168         180                                                                                                         

   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  (0, 0)

(no "SCOP Domain" information available for 2PQG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PQG)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: RIP (62)
1aRIP-2pqgB01B:26-251
1bRIP-2pqgB02B:26-251

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RIP3_MAIZE | P25891)
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIP3_MAIZE | P258912pqi 2pqj

(-) Related Entries Specified in the PDB File

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