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(-) Description

Title :  CRYSTAL STRUCTURE OF A MUTANT BETA-GLUCOSIDASE IN WHEAT COMPLEXED WITH DIMBOA-GLC
 
Authors :  M. Sue, C. Nakamura, T. Miyamoto, S. Yajima
Date :  18 May 10  (Deposition) - 16 Mar 11  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Tim Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sue, C. Nakamura, T. Miyamoto, S. Yajima
Active-Site Architecture Of Benzoxazinone-Glucoside Beta-D-Glucosidases In Triticeae
Plant Sci. V. 180 268 2011
PubMed-ID: 21421370  |  Reference-DOI: 10.1016/J.PLANTSCI.2010.09.001

(-) Compounds

Molecule 1 - BETA-GLUCOSIDASE
    Chains: A
    EC Number: 3.2.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21 CODONPLUS(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES IN UNP 50-569
    Gene: TAGLU1B
    Mutation: YES
    Organism Common: WHEAT
    Organism Scientific: TRITICUM AESTIVUM
    Organism Taxid: 4565

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2HBK1Ligand/Ion(2S)-2,4-DIHYDROXY-7-METHOXY-2H-1,4-BENZOXAZIN-3(4H)-ONE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1BGC6Ligand/IonBETA-D-GLUCOSE
2HBK6Ligand/Ion(2S)-2,4-DIHYDROXY-7-METHOXY-2H-1,4-BENZOXAZIN-3(4H)-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:43 , HIS A:145 , ASN A:190 , TYR A:334 , GLU A:407 , TRP A:455 , GLU A:462 , TRP A:463 , PHE A:471 , HOH A:590 , HBK A:600 , HOH A:702BINDING SITE FOR RESIDUE BGC A 601
2AC2SOFTWARETHR A:194 , PHE A:198 , ASP A:262 , TYR A:378 , TRP A:379 , HOH A:590 , BGC A:601 , HOH A:702BINDING SITE FOR RESIDUE HBK A 600

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:210 -A:216

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:12 -Pro A:13
2Ala A:206 -Pro A:207

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F1_2PS00653 Glycosyl hydrolases family 1 N-terminal signature.HGL1B_WHEAT82-96  1A:33-47
2GLYCOSYL_HYDROL_F1_1PS00572 Glycosyl hydrolases family 1 active site.HGL1B_WHEAT452-460  1A:403-411
Biological Unit 1 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F1_2PS00653 Glycosyl hydrolases family 1 N-terminal signature.HGL1B_WHEAT82-96  6A:33-47
2GLYCOSYL_HYDROL_F1_1PS00572 Glycosyl hydrolases family 1 active site.HGL1B_WHEAT452-460  6A:403-411

(-) Exons   (0, 0)

(no "Exon" information available for 3AIS)

(-) 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:491
 aligned with HGL1B_WHEAT | Q1XH05 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:491
                                    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       490       500       510       520       530       540       550 
          HGL1B_WHEAT    61 GPVFTKLKPWQIPKRDWFDKDFLFGASTSAYQIEGAWNEDGKGPSTWDHFCHTYPERISDMTNGDVAANSYHLYEEDVKALKDMGMKVYRFSISWSRILPDGTGKVNQAGIDYYNKLINSLIDNDIVPYVTIWHWDTPQALEDKYGGFLNRQIVDDYKQFAEVCFKNFGDRVKNWFTFNEPHTYCCFSYGEGIHAPGRCSPGMDCAVPEGDSLREPYTAGHHILLAHAEAVQLFKARYNMHGDSKIGMAFDVMGYEPYQDSFLDDQARERSIDYNMGWFLEPVVRGDYPFSMRSLIGDRLPMFTKEEQEKLASSCDIMGLNYYTSRFSKHVDMSPDFTPTLNTDDAYASSETTGSDGNDIGPITGTYWIYMYPKGLTDLLLIMKEKYGNPPVFITENGIADVEGDESMPDPLDDWKRLDYLQRHISAVKDAIDQGADVRGHFTWGLIDNFEWSLGYSSRFGLVYIDKNDGNKRKLKKSAKWFSKFNSVPKP 551
               SCOP domains d3aisa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.hhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee.hhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeeeeeeeeeeee..........hhhhhh.eeee.....................hhhhhhhhhhhhhh.....eeeee....ee...........hhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhh.ee...eee.......eeehhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------GLYCOSYL_HYDROL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ais A  12 GPVFTKLKPWQIPKRDWFDKDFLFGASTSAYQIEGAWNEDGKGPSTWDHFCHTYPERISDMTNGDVAANSYHLYEEDVKALKDMGMKVYRFSISWSRILPDGTGKVNQAGIDYYNKLINSLIDNDIVPYVTIWHWDTPQALEDKYGGFLNRQIVDDYKQFAEVCFKNFGDRVKNWFTFNAPHTYCCFSYGEGIHAPGRCSPGMDCAVPEGDSLREPYTAGHHILLAHAEAVQLFKARYNMHGDSKIGMAFDVMGYEPYQDSFLDDQARERSIDYNMGWFLEPVVRGDYPFSMRSLIGDRLPMFTKEEQEKLASSCDIMGLNYYTSRFSKHVDMSPDFTPTLNTDDAYASSETTGSDGNDIGPITGTYWIYMYPKGLTDLLLIMKEKYGNPPVFITENGIADVEGDESMPDPLDDWKRLDYLQRHISAVKDAIDQGADVRGHFTWGLIDNFEWSLGYSSRFGLVYIDKNDGNKRKLKKSAKWFSKFNSVPKP 502
                                    21        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       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AIS)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (HGL1B_WHEAT | Q1XH05)
molecular function
    GO:0008422    beta-glucosidase activity    Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
    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: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:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HGL1B_WHEAT | Q1XH05: 2dga 3aiq 3air

(-) Related Entries Specified in the PDB File

2dga THE SAME PROTEIN WITHOUT A SUBSTRATE/INHIBITOR.
3aiq
3air
3aiu
3aiv
3aiw