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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SORGHUM BICOLOR DHURRINASE 1
 
Authors :  J. Moriniere, L. Verdoucq, D. R. Bevan, A. Esen, B. Henrissat, M. Czjzek
Date :  22 Mar 04  (Deposition) - 20 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Beta-Glucosidase, Dhurrin Hydrolysis, Pest Defense, Family Gh1 (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 - DHURRINASE
    Chains: A
    EC Number: 3.2.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: SORGHUM
    Organism Scientific: SORGHUM BICOLOR MILO
    Organism Taxid: 4558
    Synonym: DHURRINASE-1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CCN1Ligand/IonACETONITRILE
3IPH1Ligand/IonPHENOL
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2CCN2Ligand/IonACETONITRILE
3IPH2Ligand/IonPHENOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:39 , HIS A:143 , ASN A:188 , ASP A:189 , TYR A:331 , TRP A:376 , GLU A:404 , TRP A:453 , GLU A:460 , TRP A:461 , PHE A:469 , CCN A:1499 , IPH A:1500BINDING SITE FOR RESIDUE BGC A1498
2AC2SOFTWARETHR A:192 , BGC A:1498 , CCN A:1499 , HOH A:2552 , HOH A:2600BINDING SITE FOR RESIDUE IPH A1500
3AC3SOFTWARETHR A:192 , TRP A:376 , BGC A:1498 , IPH A:1500 , HOH A:2599BINDING SITE FOR RESIDUE CCN A1499

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:208 -A:214

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:204 -Pro A:205
2Trp A:453 -Ser A:454

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V03)

(-) Exons   (0, 0)

(no "Exon" information available for 1V03)

(-) 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:487
 aligned with Q41290_SORBI | Q41290 from UniProtKB/TrEMBL  Length:565

    Alignment length:487
                                    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       511       521       531       541       
         Q41290_SORBI    62 IHRLSPWEIPRRDWFPPSFLFGAATSAYQIEGAWNEDGKGPSTWDHFCHNFPEWIVDRSNGDVAADSYHMYAEDVRLLKEMGMDAYRFSISWPRILPKGTLAGGINEKGVEYYNKLIDLLLENGIEPYITIFHWDTPQALVDAYGGFLDEEDYKDYTDFAKVCFEKFGKTVKNWLTFNEPETFCSVSYGTGVLAPGRCSPGVSCAVPTGNSLSEPYIVAHNLLRAHAETVDIYNKYHKGADGRIGLALNVFGRVPYTNTFLDQQAQERSMDKCLGWFLEPVVRGDYPFSMRVSARDRVPYFKEKEQEKLVGSYDMIGINYYTSTFSKHIDLSPNNSPVLNTDDAYASQETKGPDGNAIGPPTGNAWINMYPKGLHDILMTMKNKYGNPPMYITENGMGDIDKGDLPKPVALEDHTRLDYIQRHLSVLKQSIDLGADVRGYFAWSLLDNFEWSSGYTERFGIVYVDRENGCERTMKRSARWLQEFNGA 548
               SCOP domains d1v03a_ A: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1v03A00 A:11-497 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.hhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh....eeeee...eeeeee..........hhhhhh.eeee.....................hhhhhhhhhhhhhh.....eeeee....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh..ee...eee.hhhh..eeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v03 A  11 IHRLSPWEIPRRDWFPPSFLFGAATSAYQIEGAWNEDGKGPSTWDHFCHNFPEWIVDRSNGDVAADSYHMYAEDVRLLKEMGMDAYRFSISWPRILPKGTLAGGINEKGVEYYNKLIDLLLENGIEPYITIFHWDTPQALVEAYGGFLDERIIKDYTDFAKVCFEKFGKTVKNWLTFNDPETFCSVSYGTGVLAPGRCSPGVSCAVPTGNSLSEPYIVAHNLLRAHAETVDIYNKYHKGADGRIGLALNVFGRVPYTNTFLDQQAQERSMDKCLGWFLEPVVRGDYPFSMRVSARDRVPYFKEKEQEKLVGSYDMIGINYYTSTFSKHIDLSPNNSPVLNTDDAYASQETKGPDGNAIGPPTGNAWINMYPKGLHDILMTMKNKYGNPPMYITENGMGDIDKGDLPKPVALEDHTRLDYIQRHLSVLKQSIDLGADVRGYFAWSLLDNFEWSSGYTERFGIVYVDRENGCERTMKRSARWLQEFNGA 497
                                    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       490
   Legend:   → Mismatch (orange background)
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  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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V03)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q41290_SORBI | Q41290)
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.
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.

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  1v03
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 Related Entries

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

UniProtKB/TrEMBL
        Q41290_SORBI | Q41290: 1v02

(-) Related Entries Specified in the PDB File

1v02 CRYSTAL STRUCTURE OF THE SORGHUM BICOLOR DHURRINASE 1