Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF STRICTOSIDINE GLUCOSIDASE
 
Authors :  L. Barleben, S. Panjikar, M. Ruppert, J. Koepke, J. Stockigt
Date :  26 Jan 07  (Deposition) - 05 Feb 08  (Release) - 16 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Alkaloid, Glucosidase, Strictosidine, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Barleben, S. Panjikar, M. Ruppert, J. Koepke, J. Stockigt
Molecular Architecture Of Strictosidine Glucosidase - The Gateway To The Biosynthesis Of The Monoterpenoid Indole Alkaloid Family
Plant Cell V. 19 2886 2007
PubMed-ID: 17890378  |  Reference-DOI: 10.1105/TPC.106.045682

(-) Compounds

Molecule 1 - STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
    Chains: A, B
    EC Number: 3.2.1.105
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-2
    Expression System Strain: M15-PREP4
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: SERPENTWOOD
    Organism Scientific: RAUVOLFIA SERPENTINA
    Organism Taxid: 4060
    Synonym: STRICTOSIDINE GLUCOSIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2JF7)

(-) Sites  (0, 0)

(no "Site" information available for 2JF7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JF7)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:222 -Pro A:223
2Trp A:465 -Ser A:466
3Ala B:222 -Pro B:223
4Trp B:465 -Ser B:466

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JF7)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F1_2PS00653 Glycosyl hydrolases family 1 N-terminal signature.SG1_RAUSE47-61
 		  2A:47-61
B:47-61
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F1_2PS00653 Glycosyl hydrolases family 1 N-terminal signature.SG1_RAUSE47-61
 		  8A:47-61
B:47-61

(-) Exons   (0, 0)

(no "Exon" information available for 2JF7)

(-) 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:468
 aligned with SG1_RAUSE | Q8GU20 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:473
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506   
            SG1_RAUSE    37 VVHRRDFPQDFIFGAGGSAYQCEGAYNEGNRGPSIWDTFTQRSPAKISDGSNGNQAINCYHMYKEDIKIMKQTGLESYRFSISWSRVLPGGRLAAGVNKDGVKFYHDFIDELLANGIKPSVTLFHWDLPQALEDEYGGFLSHRIVDDFCEYAEFCFWEFGDKIKYWTTFNEPHTFAVNGYALGEFAPGRGGKGDEGDPAIEPYVVTHNILLAHKAAVEEYRNKFQKCQEGEIGIVLNSMWMEPLSDVQADIDAQKRALDFMLGWFLEPLTTGDYPKSMRELVKGRLPKFSADDSEKLKGCYDFIGMNYYTATYVTNAVKSNSEKLSYETDDQVTKTFERNQKPIGHALYGGWQHVVPWGLYKLLVYTKETYHVPVLYVTESGMVEENKTKILLSEARRDAERTDYHQKHLASVRDAIDDGVNVKGYFVWSFFDNFEWNLGYICRYGIIHVDYKSFERYPKESAIWYKNFIAGK 509
               SCOP domains d2jf7a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2jf7A00 A:37-509 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee.hhhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeee...eeeeee..-----..hhhhhh.eeee.........ee......eehhhhhhhhhhhhhhhhh...eeeeee...ee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh..ee...eee......eeehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------GLYCOSYL_HYDROL---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jf7 A  37 VVHRRDFPQDFIFGAGGSAYQCEGAYNEGNRGPSIWDTFTQRSPAKISDGSNGNQAINCYHMYKEDIKIMKQTGLESYRFSISWSRVLPGGRLAAGVNKDGVKFYHDFIDELLANGIKPSVTLFHWDLPQALEDEYGGFLSHRIVDDFCEYAEFCFWEFGDKIKYWTTFNEPHTFAVNGYALGEFAPGRGGKGDEGDPAIEPYVVTHNILLAHKAAVEEYRNKFQKCQEGEIGIVLNSMWMEPLSDVQADIDAQKRALDFMLGWFLEPLTTGDYPKSMRELVKGRLPKFSADDSEKLKGCYDFIGMNYYTATYVTNAV-----KLSYETDDQVTKTFERNQKPIGHALYGGWQHVVPWGLYKLLVYTKETYHVPVLYVTESGMVEENKTKILLSEARRDAERTDYHQKHLASVRDAIDDGVNVKGYFVWSFFDNFEWNLGYICRYGIIHVDYKSFERYPKESAIWYKNFIAGK 509
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       | -   |   366       376       386       396       406       416       426       436       446       456       466       476       486       496       506   
                                                                                                                                                                                                                                                                                                                                                       354   360                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:467
 aligned with SG1_RAUSE | Q8GU20 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:473
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506   
            SG1_RAUSE    37 VVHRRDFPQDFIFGAGGSAYQCEGAYNEGNRGPSIWDTFTQRSPAKISDGSNGNQAINCYHMYKEDIKIMKQTGLESYRFSISWSRVLPGGRLAAGVNKDGVKFYHDFIDELLANGIKPSVTLFHWDLPQALEDEYGGFLSHRIVDDFCEYAEFCFWEFGDKIKYWTTFNEPHTFAVNGYALGEFAPGRGGKGDEGDPAIEPYVVTHNILLAHKAAVEEYRNKFQKCQEGEIGIVLNSMWMEPLSDVQADIDAQKRALDFMLGWFLEPLTTGDYPKSMRELVKGRLPKFSADDSEKLKGCYDFIGMNYYTATYVTNAVKSNSEKLSYETDDQVTKTFERNQKPIGHALYGGWQHVVPWGLYKLLVYTKETYHVPVLYVTESGMVEENKTKILLSEARRDAERTDYHQKHLASVRDAIDDGVNVKGYFVWSFFDNFEWNLGYICRYGIIHVDYKSFERYPKESAIWYKNFIAGK 509
               SCOP domains d2jf7b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2jf7B00 B:37-509 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee.hhhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeeee..eeeeee..------.hhhhhh.eeee.........ee......eehhhhhhhhhhhhhhhhh...eeeeee...ee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh..ee...eee......eeehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------GLYCOSYL_HYDROL---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jf7 B  37 VVHRRDFPQDFIFGAGGSAYQCEGAYNEGNRGPSIWDTFTQRSPAKISDGSNGNQAINCYHMYKEDIKIMKQTGLESYRFSISWSRVLPGGRLAAGVNKDGVKFYHDFIDELLANGIKPSVTLFHWDLPQALEDEYGGFLSHRIVDDFCEYAEFCFWEFGDKIKYWTTFNEPHTFAVNGYALGEFAPGRGGKGDEGDPAIEPYVVTHNILLAHKAAVEEYRNKFQKCQEGEIGIVLNSMWMEPLSDVQADIDAQKRALDFMLGWFLEPLTTGDYPKSMRELVKGRLPKFSADDSEKLKGCYDFIGMNYYTATYVTNAV------LSYETDDQVTKTFERNQKPIGHALYGGWQHVVPWGLYKLLVYTKETYHVPVLYVTESGMVEENKTKILLSEARRDAERTDYHQKHLASVRDAIDDGVNVKGYFVWSFFDNFEWNLGYICRYGIIHVDYKSFERYPKESAIWYKNFIAGK 509
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       | -    |  366       376       386       396       406       416       426       436       446       456       466       476       486       496       506   
                                                                                                                                                                                                                                                                                                                                                       354    361
   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) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2JF7)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SG1_RAUSE | Q8GU20)
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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0050422    strictosidine beta-glucosidase activity    Catalysis of the reaction: 3alpha(S)-strictosidine + H(2)O = D-glucose + strictosidine aglycone.
biological process
    GO:0009821    alkaloid biosynthetic process    The chemical reactions and pathways resulting in the formation of alkaloids, nitrogen-containing natural products which are not otherwise classified as nonprotein amino acids, amines, peptides, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones, or primary metabolite (such as purine or pyrimidine bases).
    GO:0009820    alkaloid metabolic process    The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2jf7)
 
  Sites
(no "Sites" information available for 2jf7)
 
  Cis Peptide Bonds
    Ala A:222 - Pro A:223   [ RasMol ]  
    Ala B:222 - Pro B:223   [ RasMol ]  
    Trp A:465 - Ser A:466   [ RasMol ]  
    Trp B:465 - Ser B:466   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2jf7
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SG1_RAUSE | Q8GU20
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.105
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SG1_RAUSE | Q8GU20
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SG1_RAUSE | Q8GU20: 2jf6 3zj7 3zj8

(-) Related Entries Specified in the PDB File

2jf6 STRUCTURE OF INACTIVE MUTANT OF STRICTOSIDINE GLUCOSIDASE IN COMPLEX WITH STRICTOSIDINE