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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ZEA MAZE BETA-GLUCOSIDASE-1 IN COMPLEX WITH GLUCO-TETRAZOLE
 
Authors :  J. Moriniere, L. Verdoucq, D. R. Bevan, A. Esen, B. Henrissat, M. Czjzek
Date :  25 Mar 04  (Deposition) - 20 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Glucosidase, Glycoside Hydrolase, Dimboa-Glucoside, Inhibitor, Pest Defense, Family Gh1, Hydrolase, Chloroplast, Transit Peptide, 3D-Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Verdoucq, J. Moriniere, D. R. Bevan, A. Esen, A. Vasella, B. Henrissat, M. Czjzek
Structural Determinants Of Substrate Specificity In Family 1 Beta-Glucosidases: Novel Insights From The Crystal Structure Of Sorghum Dhurrinase-1, A Plant Beta-Glucosidase With Strict Specificity, In Complex With Its Natural Substrate
J. Biol. Chem. V. 279 31796 2004
PubMed-ID: 15148317  |  Reference-DOI: 10.1074/JBC.M402918200

(-) Compounds

Molecule 1 - BETA-GLUCOSIDASE
    Chains: A, B
    EC Number: 3.2.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Synonym: CHLOROPLAST PRECURSOR, GENTIOBIASE, CELLOBIASE, BETA-D-GLUCOSIDE GLUCOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NTZ4Ligand/IonNOJIRIMYCINE TETRAZOLE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:38 , HIS A:142 , ASN A:190 , ASP A:191 , TYR A:333 , TRP A:378 , GLU A:406 , TRP A:457 , GLU A:464 , TRP A:465 , TYR A:473 , NTZ A:1503 , HOH A:2319BINDING SITE FOR RESIDUE NTZ A1502
2AC2SOFTWARETRP A:143 , THR A:194 , TRP A:378 , GLU A:464 , PHE A:466 , NTZ A:1502 , HOH A:2449 , HOH A:2450BINDING SITE FOR RESIDUE NTZ A1503
3AC3SOFTWAREGLN B:38 , HIS B:142 , ASN B:190 , ASP B:191 , TYR B:333 , TRP B:378 , GLU B:406 , TRP B:457 , GLU B:464 , TRP B:465 , TYR B:473 , NTZ B:1503 , HOH B:2255BINDING SITE FOR RESIDUE NTZ B1502
4AC4SOFTWARETHR B:194 , PHE B:205 , TRP B:378 , GLU B:464 , NTZ B:1502 , HOH B:2388 , HOH B:2389BINDING SITE FOR RESIDUE NTZ B1503

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:210 -A:216
2B:210 -B:216

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:206 -Pro A:207
2Ala B:206 -Pro B:207

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V08)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F1_2PS00653 Glycosyl hydrolases family 1 N-terminal signature.HGGL1_MAIZE82-96
 		  2A:28-42
B:28-42
2GLYCOSYL_HYDROL_F1_1PS00572 Glycosyl hydrolases family 1 active site.HGGL1_MAIZE456-464
 		  2A:402-410
B:402-410

(-) Exons   (0, 0)

(no "Exon" information available for 1V08)

(-) 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:491
 aligned with HGGL1_MAIZE | P49235 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:491
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555 
          HGGL1_MAIZE    66 MLSPSEIPQRDWFPSDFTFGAATSAYQIEGAWNEDGKGESNWDHFCHNHPERILDGSNSDIGANSYHMYKTDVRLLKEMGMDAYRFSISWPRILPKGTKEGGINPDGIKYYRNLINLLLENGIEPYVTIFHWDVPQALEEKYGGFLDKSHKSIVEDYTYFAKVCFDNFGDKVKNWLTFNEPQTFTSFSYGTGVFAPGRCSPGLDCAYPTGNSLVEPYTAGHNILLAHAEAVDLYNKHYKRDDTRIGLAFDVMGRVPYGTSFLDKQAEERSWDINLGWFLEPVVRGDYPFSMRSLARERLPFFKDEQKEKLAGSYNMLGLNYYTSRFSKNIDISPNYSPVLNTDDAYASQEVNGPDGKPIGPPMGNPWIYMYPEGLKDLLMIMKNKYGNPPIYITENGIGDVDTKETPLPMEAALNDYKRLDYIQRHIATLKESIDLGSNVQGYFAWSLLDNFEWFAGFTERYGIVYVDRNNNCTRYMKESAKWLKEFNTAK 556
               SCOP domains d1v08a_ A: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1v08A00 A:12-502 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh...eeeee.hhhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeee...eeeeee..........hhhhhh.eeee.....................hhhhhhhhhhhhhh.....eeeee....ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh..ee...eeee.....eeeehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------GLYCOSYL_HYDROL-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_-------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v08 A  12 MLSPSEIPQRDWFPSDFTFGAATSAYQIEGAWNEDGKGESNWDHFCHNHPERILDGSNSDIGANSYHMYKTDVRLLKEMGMDAYRFSISWPRILPKGTKEGGINPDGIKYYRNLINLLLENGIEPYVTIFHWDVPQALEEKYGGFLDKSHKSIVEDYTYFAKVCFDNFGDKVKNWLTFNDPQTFTSFSYGTGVFAPGRCSPGLDCAYPTGNSLVEPYTAGHNILLAHAEAVDLYNKHYKRDDTRIGLAFDVMGRVPYGTSFLDKQAEERSWDINLGWFLEPVVRGDYPFSMRSLARERLPFFKDEQKEKLAGSYNMLGLNYYTSRFSKNIDISPNYSPVLNTDDAYASQEVNGPDGKPIGPPMGNPWIYMYPEGLKDLLMIMKNKYGNPPIYITENGIGDVDTKETPLPMEAALNDYKRLDYIQRHIATLKESIDLGSNVQGYFAWSLLDNFEWFAGFTERYGIVYVDRNNNCTRYMKESAKWLKEFNTAK 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 


Chain B from PDB  Type:PROTEIN  Length:491
 aligned with HGGL1_MAIZE | P49235 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:491
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555 
          HGGL1_MAIZE    66 MLSPSEIPQRDWFPSDFTFGAATSAYQIEGAWNEDGKGESNWDHFCHNHPERILDGSNSDIGANSYHMYKTDVRLLKEMGMDAYRFSISWPRILPKGTKEGGINPDGIKYYRNLINLLLENGIEPYVTIFHWDVPQALEEKYGGFLDKSHKSIVEDYTYFAKVCFDNFGDKVKNWLTFNEPQTFTSFSYGTGVFAPGRCSPGLDCAYPTGNSLVEPYTAGHNILLAHAEAVDLYNKHYKRDDTRIGLAFDVMGRVPYGTSFLDKQAEERSWDINLGWFLEPVVRGDYPFSMRSLARERLPFFKDEQKEKLAGSYNMLGLNYYTSRFSKNIDISPNYSPVLNTDDAYASQEVNGPDGKPIGPPMGNPWIYMYPEGLKDLLMIMKNKYGNPPIYITENGIGDVDTKETPLPMEAALNDYKRLDYIQRHIATLKESIDLGSNVQGYFAWSLLDNFEWFAGFTERYGIVYVDRNNNCTRYMKESAKWLKEFNTAK 556
               SCOP domains d1v08b_ B: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1v08B00 B:12-502 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh...eeeee.hhhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeeeeeeeeeeee..........hhhhhh.........................hhhhhhhhhhhhhhh.....eeeee....ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh..ee...eeee.....eeeehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------GLYCOSYL_HYDROL-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_-------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v08 B  12 MLSPSEIPQRDWFPSDFTFGAATSAYQIEGAWNEDGKGESNWDHFCHNHPERILDGSNSDIGANSYHMYKTDVRLLKEMGMDAYRFSISWPRILPKGTKEGGINPDGIKYYRNLINLLLENGIEPYVTIFHWDVPQALEEKYGGFLDKSHKSIVEDYTYFAKVCFDNFGDKVKNWLTFNDPQTFTSFSYGTGVFAPGRCSPGLDCAYPTGNSLVEPYTAGHNILLAHAEAVDLYNKHYKRDDTRIGLAFDVMGRVPYGTSFLDKQAEERSWDINLGWFLEPVVRGDYPFSMRSLARERLPFFKDEQKEKLAGSYNMLGLNYYTSRFSKNIDISPNYSPVLNTDDAYASQEVNGPDGKPIGPPMGNPWIYMYPEGLKDLLMIMKNKYGNPPIYITENGIGDVDTKETPLPMEAALNDYKRLDYIQRHIATLKESIDLGSNVQGYFAWSLLDNFEWFAGFTERYGIVYVDRNNNCTRYMKESAKWLKEFNTAK 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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V08)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HGGL1_MAIZE | P49235)
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:0009736    cytokinin-activated signaling pathway    A series of molecular signals generated by the binding of a cytokinin to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
    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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  1v08
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  3.2.1.21
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 Related Entries

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

UniProtKB/Swiss-Prot
        HGGL1_MAIZE | P49235: 1e1e 1e1f 1e4l 1e4n 1e55 1e56 1h49 1hxj

(-) Related Entries Specified in the PDB File

1e1e CRYSTAL STRUCTURE OF A MONOCOT (MAIZE ZMGLU1 ) BETA-GLUCOSIDASE
1e1f CRYSTAL STRUCTURE OF A MONOCOT (MAIZE ZMGLU1 ) BETA-GLUCOSIDASE IN COMPLEX WITH P- NITROPHENYL-BETA-D-THIOGLUCOSIDE
1e4l CRYSTAL STRUCTURE OF THE INACTIVE MUTANT MONOCOT(MAIZE ZMGLU1) BETA-GLUCOSIDASE ZM GLU191ASP
1e4n CRYSTAL STRUCTURE OF THE INACTIVE MUTANT MONOCOT(MAIZE ZMGLU1) BETA-GLUCOSIDASE ZMGLU E191D IN COMPLEX WITHTHE NATURAL AGLYCONE DIMBOA
1e55 CRYSTAL STRUCTURE OF THE INACTIVE MUTANT MONOCOT(MAIZE ZMGLU1) BETA-GLUCOSIDASE ZMGLUE191D IN COMPLEX WITHTHE COMPETITIVE INHIBITOR DHURRIN
1e56 CRYSTAL STRUCTURE OF THE INACTIVE MUTANT MONOCOT(MAIZE ZMGLU1) BETA-GLUCOSIDASE ZMGLUE191D IN COMPLEX WITHTHE NATURAL SUBSTRATE DIMBOA-BETA-D-GLUCOSIDE
1h49 CRYSTAL STRUCURE OF THE INACTIVE DOUBLE MUTANT OF THE MAIZE BETA-GLUCOSIDASE ZMGLU1 -E191D-F198V IN COMPLEX WITH DIMBOA- GLUCOSIDE
1hxj CRYSTAL STRUCTURE OF THE MAIZE ZM-P60.1 BETA-GLUCOSIDASE