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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-GLUCOSIDASE FROM TERMITE NEOTERMES KOSHUNENSIS IN COMPLEX WITH A NEW GLUCOPYRANOSIDIC PRODUCT
 
Authors :  W. Y. Jeng, C. I. Liu, A. H. J. Wang
Date :  03 Oct 11  (Deposition) - 04 Jul 12  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.13
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Cellulases, Glycosyl Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Y. Jeng, N. C. Wang, C. T. Lin, W. J. Chang, C. I. Liu, A. H. J. Wang
High-Resolution Structures Of Neotermes Koshunensis Beta-Glucosidase Mutants Provide Insights Into The Catalyti Mechanism And The Synthesis Of Glucoconjugates
Acta Crystallogr. , Sect. D V. 68 829 2012
PubMed-ID: 22751668  |  Reference-DOI: 10.1107/S0907444912013224

(-) Compounds

Molecule 1 - BETA-GLUCOSIDASE
    Chains: A
    EC Number: 3.2.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL-21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NKBG
    Mutation: YES
    Organism Scientific: NEOTERMES KOSHUNENSIS
    Organism Taxid: 60586

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GBH1Ligand/Ion2-{4-[2-(BETA-D-GLUCOPYRANOSYLOXY)ETHYL]PIPERAZIN-1-YL}ETHANESULFONIC ACID
3GOL1Ligand/IonGLYCEROL
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GBH1Ligand/Ion2-{4-[2-(BETA-D-GLUCOPYRANOSYLOXY)ETHYL]PIPERAZIN-1-YL}ETHANESULFONIC ACID
3GOL1Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GBH2Ligand/Ion2-{4-[2-(BETA-D-GLUCOPYRANOSYLOXY)ETHYL]PIPERAZIN-1-YL}ETHANESULFONIC ACID
3GOL2Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:45 , HIS A:148 , ASN A:192 , ASP A:193 , THR A:196 , TYR A:337 , TRP A:374 , GLU A:402 , TRP A:444 , GLU A:451 , TRP A:452 , PHE A:460 , HOH A:1010 , HOH A:1100 , HOH A:1103 , HOH A:1116 , HOH A:1179 , HOH A:1193 , HOH A:1195BINDING SITE FOR RESIDUE GBH A 507
2AC2SOFTWAREASN A:303 , GLU A:307 , GLU A:350 , ARG A:355 , HOH A:805 , HOH A:1148 , HOH A:1185BINDING SITE FOR RESIDUE GOL A 508
3AC3SOFTWARELYS A:179 , ASN A:180 , HOH A:929BINDING SITE FOR RESIDUE NA A 509
4AC4SOFTWAREHOH A:613 , HOH A:969BINDING SITE FOR RESIDUE CL A 510
5AC5SOFTWAREASN A:262BINDING SITE FOR RESIDUE CL A 511

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VIN)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:208 -Pro A:209
2Glu A:350 -Pro A:351
3Trp A:444 -Ser A:445

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VIN)

(-) Exons   (0, 0)

(no "Exon" information available for 3VIN)

(-) 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:472
 aligned with Q8T0W7_9NEOP | Q8T0W7 from UniProtKB/TrEMBL  Length:498

    Alignment length:472
                                    36        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  
         Q8T0W7_9NEOP    27 TVYTFPDEFKLGAATASYQIEGAWDENGKGPNIWDTLTHEHPDYVVDGATGDIADDSYHLYKEDVKILKELGAQVYRFSISWARVLPEGHDNIVNQDGIDYYNNLINELLANGIEPMVTMYHWDLPQALQDLGGWPNLVLAKYSENYARVLFKNFGDRVKLWLTFNEPLTFMDGYASEIGMAPSINTPGIGDYLAAHTVIHAHARIYHLYDQEFRAEQGGKVGISLNINWCEPATNSAEDRASCENYQQFNLGLYAHPIFTEEGDYPAVLKDRVSRNSADEGYTDSRLPQFTAEEVEYIRGTHDFLGINFYTALLGKSGVEGYEPSRYRDSGVILTQDAAWPISASSWLKVVPWGFRKELNWIKNEYNNPPVFITENGFSDYGGLNDTGRVHYYTEHLKEMLKAIHEDGVNVIGYTAWSLMDNFEWLRGYSEKFGIYAVDFEDPARPRIPKESAKVLAEIMNTRKIPERFRD 498
               SCOP domains d3vina_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.hhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..eeeee.hhhhhh........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhh.......hhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..........hhhhhhhhh....eeeee...eeeee........hhhhhhh.eee...............hhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhhhhh....eeeeeee......hhhhh.......eee........eeehhhhhhhhhhhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vin A  27 TVYTFPDEFKLGAATASYQIEGAWDENGKGPNIWDTLTHEHPDYVVDGATGDIADDSYHLYKEDVKILKELGAQVYRFSISWARVLPEGHDNIVNQDGIDYYNNLINELLANGIEPMVTMYHWDLPQALQDLGGWPNLVLAKYSENYARVLFKNFGDRVKLWLTFNDPLTFMDGYASEIGMAPSINTPGIGDYLAAHTVIHAHARIYHLYDQEFRAEQGGKVGISLNINWCEPATNSAEDRASCENYQQFNLGLYAHPIFTEEGDYPAVLKDRVSRNSADEGYTDSRLPQFTAEEVEYIRGTHDFLGINFYTALLGKSGVEGYEPSRYRDSGVILTQDAAWPISASSWLKVVPWGFRKELNWIKNEYNNPPVFITENGFSDYGGLNDTGRVHYYTEHLKEMLKAIHEDGVNVIGYTAWSLMDNFEWLRGYSEKFGIYAVDFEDPARPRIPKESAKVLAEIMNTRKIPERFRD 498
                                    36        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
   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 3VIN)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8T0W7_9NEOP | Q8T0W7)
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.

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  3.2.1.21
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 Related Entries

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

UniProtKB/TrEMBL
        Q8T0W7_9NEOP | Q8T0W7: 3ahz 3ai0 3vif 3vig 3vih 3vii 3vij 3vik 3vil 3vim 3vio 3vip

(-) Related Entries Specified in the PDB File

3ahz 3ai0 3vif 3vig 3vih 3vii 3vij 3vik 3vil 3vim 3vio 3vip