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(-) Description

Title :  CRYSTAL STRUCTURE OF SAPORIN-L1 IN COMPLEX WITH THE TRINUCLEOTIDE INHIBITOR, A TRANSITION STATE ANALOGUE
 
Authors :  M. Ho, M. B. Sturm, S. C. Almo, V. L. Schramm
Date :  20 May 09  (Deposition) - 08 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transition State, Ribosome Inactivating Proteins, Rips, Hydrolase, 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 - VACUOLAR SAPORIN
    Chains: A, B
    EC Number: 3.2.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1TXN2Ligand/Ion(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-3,6-DIHYDRO-9H-PURIN-9-YL)-2-({[(S)-({(3R,4R)-4-({[(S)-{[(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-6,8-DIHYDRO-9H-PURIN-9-YL)-2-(HYDROXYMETHYL)-4-METHOXYTETRAHYDROFURAN-3-YL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]PYRROLIDIN-3-YL}OXY)(HYDROXY)PHOSPHORYL]OXY}METHYL)-4-METHOXYTETRAHYDROFURAN-3-YL 3-HYDROXYPROPYL HYDROGEN(S)-PHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1TXN1Ligand/Ion(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-3,6-DIHYDRO-9H-PURIN-9-YL)-2-({[(S)-({(3R,4R)-4-({[(S)-{[(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-6,8-DIHYDRO-9H-PURIN-9-YL)-2-(HYDROXYMETHYL)-4-METHOXYTETRAHYDROFURAN-3-YL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]PYRROLIDIN-3-YL}OXY)(HYDROXY)PHOSPHORYL]OXY}METHYL)-4-METHOXYTETRAHYDROFURAN-3-YL 3-HYDROXYPROPYL HYDROGEN(S)-PHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1TXN1Ligand/Ion(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-3,6-DIHYDRO-9H-PURIN-9-YL)-2-({[(S)-({(3R,4R)-4-({[(S)-{[(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-6,8-DIHYDRO-9H-PURIN-9-YL)-2-(HYDROXYMETHYL)-4-METHOXYTETRAHYDROFURAN-3-YL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]PYRROLIDIN-3-YL}OXY)(HYDROXY)PHOSPHORYL]OXY}METHYL)-4-METHOXYTETRAHYDROFURAN-3-YL 3-HYDROXYPROPYL HYDROGEN(S)-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:71 , LEU A:72 , TYR A:73 , VAL A:74 , PHE A:94 , GLU A:121 , TYR A:123 , PRO A:124 , GLU A:174 , ARG A:177 , GLU A:206 , ASN A:207 , TRP A:209 , GLY A:210 , ARG A:214 , TYR A:233 , LEU A:254 , HOH A:261 , HOH A:270 , HOH A:302 , THR B:231 , SER B:232 , TYR B:233 , HOH B:272BINDING SITE FOR RESIDUE TXN A 258
2AC2SOFTWARETHR A:231 , SER A:232 , TYR A:233 , ASN B:71 , LEU B:72 , TYR B:73 , VAL B:74 , PHE B:94 , GLU B:121 , SER B:122 , TYR B:123 , PRO B:124 , GLU B:174 , ARG B:177 , GLU B:206 , ASN B:207 , TRP B:209 , GLY B:210 , ARG B:214 , TYR B:233 , LEU B:254 , HOH B:262 , HOH B:263BINDING SITE FOR RESIDUE TXN B 258

(-) SS Bonds  (0, 0)

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

(-) 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 3HIV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HIV)

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

    Alignment length:257
                                    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       
         Q2QEH4_SAPOF    22 VIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLYVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 278
               SCOP domains d3hiva_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3hivA01 A:1-176 Ricin (A subunit), domain 1                                                                                                                                     3hivA02 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.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeeeeee.........eeeee.hhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hiv A   1 VIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLYVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 257
                                    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       


Chain B from PDB  Type:PROTEIN  Length:257
 aligned with Q2QEH4_SAPOF | Q2QEH4 from UniProtKB/TrEMBL  Length:299

    Alignment length:257
                                    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       
         Q2QEH4_SAPOF    22 VIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLYVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 278
               SCOP domains d3hivb_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3hivB01 B:1-176 Ricin (A subunit), domain 1                                                                                                                                     3hivB02 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..........hhhhhhhhhhhhhhhhhhhh....eeeeeeee.........eeeee.hhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hiv B   1 VIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLYVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 257
                                    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
   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 3HIV)

(-) 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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  3.2.2.22
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3hio
3hiq
3his SAME PROTEIN, APO FORM
3hit SAME PROTEIN IN COMPLEX WITH DINUCLEOTIDE INHIBITOR
3hiw