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(-) Description

Title :  CRYSTAL STRUCTURE OF NATURAL CINNAMOMIN (ISOFORM III)
 
Authors :  A. Azzi, T. Wang, D. -W. Zhu, Y. -S. Zou, W. -Y. Liu, S. -X. Lin
Date :  11 Jan 08  (Deposition) - 10 Feb 09  (Release) - 10 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribosome Inhibiting Proteins, Toxin, Hydrolase, Cinnamomin, Plant Defense, N-Glycosidase, Protein Synthesis Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Azzi, T. Wang, D. -W. Zhu, Y. -S. Zou, W. -Y. Liu, S. -X. Lin
Crystal Structure Of Native Cinnamomin Isoform Iii And Its Comparison With Other Ribosome Inactivating Proteins.
Proteins: Struct. , Funct. , V. 74 250 2009 Bioinf.
PubMed-ID: 18837036  |  Reference-DOI: 10.1002/PROT.22251

(-) Compounds

Molecule 1 - TYPE 2 RIBOSOME-INACTIVATING PROTEIN CINNAMOMIN III
    Chains: A, B
    EC Number: 3.2.2.22
    Fragment: RESIDUES 11-580
    Organ: SEEDS
    Organism Common: CAMPHOR TREE
    Organism Scientific: CINNAMOMUM CAMPHORA
    Organism Taxid: 13429
    Other Details: DIACETYL-GLUCOSAMINE (AS5), MANNOSE (BMA) AND XYLOSE (XYS)
    Other Details - Source: NATURAL
    Synonym: CINNAMOMIN

 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  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1AS56Ligand/Ion2-(ACETYLAMINO)-4-O-[2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GULOPYRANOSYL]-1,5-ANHYDRO-2-DEOXY-D-MANNITOL
2BMA2Ligand/IonBETA-D-MANNOSE
3XYP1Ligand/IonBETA-D-XYLOPYRANOSE
4XYS1Ligand/IonXYLOPYRANOSE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1AS53Ligand/Ion2-(ACETYLAMINO)-4-O-[2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GULOPYRANOSYL]-1,5-ANHYDRO-2-DEOXY-D-MANNITOL
2BMA1Ligand/IonBETA-D-MANNOSE
3XYP1Ligand/IonBETA-D-XYLOPYRANOSE
4XYS-1Ligand/IonXYLOPYRANOSE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1AS53Ligand/Ion2-(ACETYLAMINO)-4-O-[2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GULOPYRANOSYL]-1,5-ANHYDRO-2-DEOXY-D-MANNITOL
2BMA1Ligand/IonBETA-D-MANNOSE
3XYP-1Ligand/IonBETA-D-XYLOPYRANOSE
4XYS1Ligand/IonXYLOPYRANOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:295 , ASN A:420 , BMA A:1552 , XYP A:1553BINDING SITE FOR RESIDUE AS5 A1549
02AC2SOFTWAREASN A:10BINDING SITE FOR RESIDUE AS5 A1550
03AC3SOFTWARETRP A:378 , ALA A:379 , ASN A:380 , TYR A:410 , HOH A:2068BINDING SITE FOR RESIDUE AS5 A1551
04AC4SOFTWARETHR B:295 , THR B:335 , AS5 B:1550BINDING SITE FOR RESIDUE BMA B1549
05AC5SOFTWAREPRO B:220 , ASN B:285 , THR B:295 , SER B:328 , LEU B:333 , ASN B:420 , BMA B:1549 , XYS B:1553BINDING SITE FOR RESIDUE AS5 B1550
06AC6SOFTWAREASN B:10 , HOH B:2050BINDING SITE FOR RESIDUE AS5 B1551
07AC7SOFTWAREASN A:398 , GLN B:213 , TRP B:378 , ALA B:379 , ASN B:380 , TYR B:410 , HOH B:2051BINDING SITE FOR RESIDUE AS5 B1552
08AC8SOFTWAREAS5 A:1549 , XYP A:1553BINDING SITE FOR RESIDUE BMA A1552
09AC9SOFTWAREAS5 A:1549 , BMA A:1552 , SER B:83BINDING SITE FOR RESIDUE XYP A1553
10BC1SOFTWARESER B:227 , AS5 B:1550BINDING SITE FOR RESIDUE XYS B1553

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:251 -A:289
2A:305 -A:324
3A:348 -A:365
4A:436 -A:449
5A:475 -A:493
6B:251 -B:289
7B:305 -B:324
8B:348 -B:365
9B:436 -B:449
10B:475 -B:493

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn B:285 -Asp B:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VLC)

(-) Exons   (0, 0)

(no "Exon" information available for 2VLC)

(-) 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:518
 aligned with Q94BW3_CINCA | Q94BW3 from UniProtKB/TrEMBL  Length:580

    Alignment length:548
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572        
         Q94BW3_CINCA    33 YQTVTFTTKNATKTSYTQFIEALRAQLASGEEPHGIPVMRERSTVPDSKRFILVELSNWAADSPVTLAVDVTNAYVVAYRTGSQSFFLREDNPDPAIENLLPDTKRYTFPFSGSYTDLERVAGERREEILLGMDPLENAISALWISNLNQQRALARSLIVVIQMVAEAVRFRFIEYRVRESITRAEMFRPDPAMLSLENKWSALSNAVQQSNQGGVFSSPVELRSISNKPVYVGSVSDRVISGLAIMLFICRSTDRASSDQFIDHLLMIRPILADVADVATDADNDDTCADPEPTVRISGRNGLCVDVRDGKYNNGNPIQLWPCKQNSDVNQLWTLRRDGTIRSNGKCLTTNGYSAGDYVMIYDCRTPVTAASIWQFWANGTIINPQSALVLSAESGNPRTTLTVQADIYASRQGWLAGNNTEPFVTSIVGFNDLCMQANGDAMWVVECESSKAEQKWALYPDGSIRPHQDRDRCLTSTDNHSQGSIIIISSCSPGSEGQRWVFMNDGTILNLKNGLVMDVKGSDPSLHQIIIWPATGKPNQKWLPLL 580
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhh.eeeeeee.......eeeeee.....eeeeee..eeeeee.................eeeeee.hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....eeeeee..hhhhhh...........------------------------------..........ee.eee.hhheeee.hhh......eeee......hhhhheee.....eee..eeeee........eeee......hhhh..ee.....eee....eeee..........eee....hhhh.eee......eee.eehhh.eeeeee..eeeeee.........eee.....eee.....eeeee.........eeeee....hhhhh................eeee.hhhhhhh.eeee....hhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vlc A   1 YQTVTFTTKNATKTSYTQFIEALRAQLASGEEPHGIPVMRERSTVPDSKRFILVELSNWAADSPVTLAVDVTNAYVVAYRTGSQSFFLREDNPDPAIENLLPDTKRYTFPFSGSYTDLERVAGERREEILLGMDPLENAISALWISNLNQQRALARSLIVVIQMVAEAVRFRFIEYRVRESISRAEMFRPDPAMLSLENKWSALSNAVQQSNQGGVFSSPVELRSISNKPVYVGSVSDRVISGLAIMLFICRST------------------------------NDDTCADPEPTVRISGRNGLCVRVRDGKYNNGNPIQLWPCKQNSDVNQLWTLRRDGTIRSNGKCLTTNGYSAGDYVMIYDCRTPVTAASIWQFWANGTIINPQSALVLSAESGNPRTTLTVQADIYASRQGWLAGNNTEPFVTSIVGFNDLCMQANGDAMWVVECESSKAEQKWALYPDGSIRPHQDRDRCLTSTDNHSQGSIIIISSCSPGSEGQRWVFMNDGTILNLKNGLVMDVKGSDPSLHQIIIWPATGKPNQKWLPLL 548
                                    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   |     -         -         -    |  290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540        
                                                                                                                                                                                                                                                                                       254                            285                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:518
 aligned with Q94BW3_CINCA | Q94BW3 from UniProtKB/TrEMBL  Length:580

    Alignment length:548
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572        
         Q94BW3_CINCA    33 YQTVTFTTKNATKTSYTQFIEALRAQLASGEEPHGIPVMRERSTVPDSKRFILVELSNWAADSPVTLAVDVTNAYVVAYRTGSQSFFLREDNPDPAIENLLPDTKRYTFPFSGSYTDLERVAGERREEILLGMDPLENAISALWISNLNQQRALARSLIVVIQMVAEAVRFRFIEYRVRESITRAEMFRPDPAMLSLENKWSALSNAVQQSNQGGVFSSPVELRSISNKPVYVGSVSDRVISGLAIMLFICRSTDRASSDQFIDHLLMIRPILADVADVATDADNDDTCADPEPTVRISGRNGLCVDVRDGKYNNGNPIQLWPCKQNSDVNQLWTLRRDGTIRSNGKCLTTNGYSAGDYVMIYDCRTPVTAASIWQFWANGTIINPQSALVLSAESGNPRTTLTVQADIYASRQGWLAGNNTEPFVTSIVGFNDLCMQANGDAMWVVECESSKAEQKWALYPDGSIRPHQDRDRCLTSTDNHSQGSIIIISSCSPGSEGQRWVFMNDGTILNLKNGLVMDVKGSDPSLHQIIIWPATGKPNQKWLPLL 580
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----RIP-2vlcB05 B:5-211                                                                                                                                                                                            -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2vlcB01 B:423-544                                                                                          ---- Pfam domains (1)
           Pfam domains (2) ----RIP-2vlcB06 B:5-211                                                                                                                                                                                            -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2vlcB02 B:423-544                                                                                          ---- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2vlcB03 B:423-544                                                                                          ---- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2vlcB04 B:423-544                                                                                          ---- Pfam domains (4)
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhh.eeeeeee.......eeeeee.....eeeeee..eeee...................ee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....eeeeee..hhhhhh...........------------------------------..........ee.eee.hhheeee.hhh......eeee......hhhhheee.....eee..eeeee........eeee......hhhh..ee.....eee....eeee..........eee....hhhh.eee......eee.eee...eeeeee..eeeeee.........eee.....eee.....eeeee.........eeeee....hhhhh................eeee.hhhhhhh.eeee....hhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vlc B   1 YQTVTFTTKNATKTSYTQFIEALRAQLASGEEPHGIPVMRERSTVPDSKRFILVELSNWAADSPVTLAVDVTNAYVVAYRTGSQSFFLREDNPDPAIENLLPDTKRYTFPFSGSYTDLERVAGERREEILLGMDPLENAISALWISNLNQQRALARSLIVVIQMVAEAVRFRFIEYRVRESISRAEMFRPDPAMLSLENKWSALSNAVQQSNQGGVFSSPVELRSISNKPVYVGSVSDRVISGLAIMLFICRST------------------------------NDDTCADPEPTVRISGRNGLCVRVRDGKYNNGNPIQLWPCKQNSDVNQLWTLRRDGTIRSNGKCLTTNGYSAGDYVMIYDCRTPVTAASIWQFWANGTIINPQSALVLSAESGNPRTTLTVQADIYASRQGWLAGNNTEPFVTSIVGFNDLCMQANGDAMWVVECESSKAEQKWALYPDGSIRPHQDRDRCLTSTDNHSQGSIIIISSCSPGSEGQRWVFMNDGTILNLKNGLVMDVKGSDPSLHQIIIWPATGKPNQKWLPLL 548
                                    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   |     -         -         -    |  290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540        
                                                                                                                                                                                                                                                                                       254                            285
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: Trefoil (131)
(-)
Clan: no clan defined [family: RIP] (62)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q94BW3_CINCA | Q94BW3)
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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