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(-) Description

Title :  CRYSTAL STRUCTURE OF A RICE OS3BGLU6 BETA-GLUCOSIDASE WITH COVALENTLY BOUND 2-DEOXY-2-FLUOROGLUCOSIDE TO THE CATALYTIC NUCLEOPHILE E396
 
Authors :  S. Seshadri, T. Akiyama, R. Opassiri, B. Kuaprasert, J. R. K. Cairns
Date :  17 Mar 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha Barrel, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Seshadri, T. Akiyama, R. Opassiri, B. Kuaprasert, J. R. K. Cairns
Structural And Enzymatic Characterization Of Os3Bglu6, A Rice Beta-Glucosidase Hydrolyzing Hydrophobic Glycosides An (1->3)- And (1->2)-Linked Disaccharides.
Plant Physiol. V. 151 47 2009
PubMed-ID: 19587102  |  Reference-DOI: 10.1104/PP.109.139436

(-) Compounds

Molecule 1 - OS03G0212800 PROTEIN
    Chains: A
    EC Number: 3.2.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A+/DEST
    Expression System Strain: ORIGAMI(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 38-521
    Organism Common: RICE
    Organism Scientific: ORYZA SATIVA SUBSP. JAPONICA
    Organism Taxid: 39947
    Synonym: BETA-GLUCOSIDASE, GLYCOSYL HYDROLASE FAMILY 1 PROTEIN, EXPRESSED

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1G2F1Ligand/Ion2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANOSE
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:31 , HIS A:132 , ASN A:177 , GLU A:178 , TYR A:321 , TRP A:366 , GLU A:394 , TRP A:444 , GLU A:451 , TRP A:452 , PHE A:460 , HOH A:744 , HOH A:857BINDING SITE FOR RESIDUE G2F A 1001
2AC2SOFTWAREASN A:402 , PRO A:403 , ILE A:405 , ILE A:407 , PHE A:464 , LYS A:468 , HOH A:511 , HOH A:875 , HOH A:896BINDING SITE FOR RESIDUE GOL A 1002
3AC3SOFTWAREALA A:80 , GLY A:83 , MET A:84 , ASP A:85 , LYS A:122 , HOH A:930BINDING SITE FOR RESIDUE GOL A 1003

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:197 -A:205

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:193 -Pro A:194
2Trp A:444 -Ser A:445

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F1_2PS00653 Glycosyl hydrolases family 1 N-terminal signature.BGL06_ORYSJ54-68  1A:21-35

(-) Exons   (0, 0)

(no "Exon" information available for 3GNR)

(-) Sequences/Alignments

Asymmetric/Biological 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:478
 aligned with BGL06_ORYSJ | Q8L7J2 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:478
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513        
          BGL06_ORYSJ    44 GLTRGSFPEGFVFGTASAAYQYEGAVKEDGRGQTIWDTFAHTFGKITDFSNADVAVDQYHRFEEDIQLMADMGMDAYRFSIAWSRIYPNGVGQVNQAGIDHYNKLIDALLAKGIQPYVTLYHWDLPQALEDKYKGWLDRQIVDDFAAYAETCFREFGDRVKHWITLNEPHTVAIQGYDAGLQAPGRCSVLLHLYCKAGNSGTEPYVVAHHFILAHAAAASIYRTKYKATQNGQLGIAFDVMWFEPMSNTTIDIEAAKRAQEFQLGWFADPFFFGDYPATMRARVGERLPRFTADEAAVVKGALDFVGINHYTTYYTRHNNTNIIGTLLNNTLADTGTVSLPFKNGKPIGDRANSIWLYIVPRGMRSLMNYVKERYNSPPVYITENGMDDSNNPFISIKDALKDSKRIKYHNDYLTNLAASIKEDGCDVRGYFAWSLLDNWEWAAGYSSRFGLYFVDYKDNLKRYPKNSVQWFKALLKT 521
               SCOP domains d3gnra_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3gnrA00 A:11-488 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....eeeee.hhhhhh..........hhhhhhhh...............hhhhhhhhhhhhhhh....eeeee.hhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh....eeeee...eeeeee...........hhhhhh.eeee.ee..ee.............hhhhhhhhhhhhhhhh...eeeeee...ee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeeeeee......hhhhhh.ee...eee.......eeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------GLYCOSYL_HYDROL--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gnr A  11 GLTRGSFPEGFVFGTASAAYQYEGAVKEDGRGQTIWDTFAHTFGKITDFSNADVAVDQYHRFEEDIQLMADMGMDAYRFSIAWSRIYPNGVGQVNQAGIDHYNKLIDALLAKGIQPYVTLYHWDLPQALEDKYKGWLDRQIVDDFAAYAETCFREFGDRVKHWITLNEPHTVAIQGYDAGLQAPGRCSVLLHLYCKAGNSGTEPYVVAHHFILAHAAAASIYRTKYKATQNGQLGIAFDVMWFEPMSNTTIDIEAAKRAQEFQLGWFADPFFFGDYPATMRARVGERLPRFTADEAAVVKGALDFVGINHYTTYYTRHNNTNIIGTLLNNTLADTGTVSLPFKNGKPIGDRANSIWLYIVPRGMRSLMNYVKERYNSPPVYITENGMDDSNNPFISIKDALKDSKRIKYHNDYLTNLAASIKEDGCDVRGYFAWSLLDNWEWAAGYSSRFGLYFVDYKDNLKRYPKNSVQWFKALLKT 488
                                    20        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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BGL06_ORYSJ | Q8L7J2)
molecular function
    GO:0033907    beta-D-fucosidase activity    Catalysis of the hydrolysis of terminal non-reducing beta-D-fucose residues in beta-D-fucosides.
    GO:0004565    beta-galactosidase activity    Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
    GO:0080083    beta-gentiobiose beta-glucosidase activity    Catalysis of the hydrolysis of glucosidic link in beta-gentiobiose.
    GO:0008422    beta-glucosidase activity    Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
    GO:0080079    cellobiose glucosidase activity    Catalysis of the reaction: cellobiose + H2O = 2 D-glucose.
    GO:0042973    glucan endo-1,3-beta-D-glucosidase activity    Catalysis of the hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans.
    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:0102483    scopolin beta-glucosidase activity    Catalysis of the reaction: H2O + scopolin <=> beta-D-glucose + scopoletin
biological process
    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:1901657    glycosyl compound metabolic process    The chemical reactions and pathways involving glycosyl compound.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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UniProtKB/Swiss-Prot
        BGL06_ORYSJ | Q8L7J2: 3gno 3gnp 3wba 3wbe

(-) Related Entries Specified in the PDB File

3gno CRYSTAL STRUCTURE OF A RICE OS3BGLU6 BETA-GLUCOSIDASE
3gnp CRYSTAL STRUCTURE OF A RICE OS3BGLU6 BETA-GLUCOSIDASE WITH OCTYL-BETA-D-THIO-GLUCOSIDE