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(-) Description

Title :  CRYSTAL STRUCTURE OF SAPORIN-L1 MUTANT (Y73A) FROM SAPONARIA OFFICINALIS
 
Authors :  M. Ho, M. B. Sturm, S. C. Almo, V. L. Schramm
Date :  20 May 09  (Deposition) - 08 Dec 09  (Release) - 21 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribosome Inactivating Proteins, Rips, Hydrolase, Plant Defense, Protein Synthesis Inhibitor, Toxin (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 - VACUOLAR SAPORIN
    Chains: A, B
    EC Number: 3.2.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET100D
    Expression System Strain: ROSETTA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: COMMON SOAPWORT
    Organism Scientific: SAPONARIA OFFICINALIS
    Organism Taxid: 3572

 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 3HIQ)

(-) Sites  (0, 0)

(no "Site" information available for 3HIQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Arg A:44 -Pro A:45
2Gly A:47 -Pro A:48
3Pro A:48 -Pro A:49
4Glu A:196 -Pro A:197
5Arg B:44 -Pro B:45
6Gly B:47 -Pro B:48
7Pro B:48 -Pro B:49
8Glu B:196 -Pro B:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HIQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3HIQ)

(-) 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:259
 aligned with Q2QEH4_SAPOF | Q2QEH4 from UniProtKB/TrEMBL  Length:299

    Alignment length:259
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269         
         Q2QEH4_SAPOF    20 TAVIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLYVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 278
               SCOP domains d3hiqa_ A: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3hiqA01 A:-1-176 Ricin (A subunit), domain 1                                                                                                                                      3hiqA02 A:177-257 Ricin (A Subunit), domain 2                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhhhhhh......................eeeeeee....eeeeeee.....eeeeeee.....eeeee......hhhhhhhhhhhhhhhh.eee.....hhhhhhhhhh.hhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh....eeeeeeee.........eeeee.hhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hiq A  -1 FTVIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLAVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 257
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248         


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with Q2QEH4_SAPOF | Q2QEH4 from UniProtKB/TrEMBL  Length:299

    Alignment length:258
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270        
         Q2QEH4_SAPOF    21 AVIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLYVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 278
               SCOP domains d3hiqb_ B: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3hiqB01 B:0-176 Ricin (A subunit), domain 1                                                                                                                                      3hiqB02 B:177-257 Ricin (A Subunit), domain 2                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhhhhhhh......................eeeeeeee..eeeeeeee.....eeeeeee.....eeeee......hhhhhhhhhhhhhhhh.eee.....hhhhhhhhhh.hhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........eeeee.hhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hiq B   0 TVIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLAVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 257
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q2QEH4_SAPOF | Q2QEH4)
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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  Cis Peptide Bonds
    Arg A:44 - Pro A:45   [ RasMol ]  
    Arg B:44 - Pro B:45   [ RasMol ]  
    Glu A:196 - Pro A:197   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q2QEH4_SAPOF | Q2QEH4: 3his 3hit 3hiv 3hiw

(-) Related Entries Specified in the PDB File

3hio 3his 3hit 3hiv 3hiw