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(-) Description

Title :  STRUCTURE OF BETA-GLUCOSIDASE 3B FROM THERMOTOGA NEAPOLITANA IN COMPLEX WITH ALPHA-D-GLUCOSE
 
Authors :  T. Pozzo, E. N. Karlsson, D. T. Logan
Date :  28 Jan 10  (Deposition) - 09 Feb 10  (Release) - 23 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Tim Barrel Fold, Fibronectin Type Iii Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Pozzo, J. Linares Pasten, E. N. Karlsson, D. T. Logan
Structural And Functional Analysis Of Beta-Glucosidase 3B From Thermotoga Neapolitana: A Thermostable 3-Domain Representative Of Glycoside Hydrolase Family 3
J. Mol. Biol. V. 397 724 2010
PubMed-ID: 20138890  |  Reference-DOI: 10.1016/J.JMB.2010.01.072
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-GLUCOSIDASE
    Chains: A
    EC Number: 3.2.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TUNER(DE3)
    Expression System Taxid: 562
    Expression System Vector: PET-22B
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMOTOGA NEAPOLITANA
    Organism Taxid: 309803
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Strain: DSM 4359
    Synonym: BETA-GLUCOSIDASE 3B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1BR4Ligand/IonBROMIDE ION
2GLC1Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:58 , LEU A:116 , ARG A:130 , LYS A:163 , HIS A:164 , ARG A:174 , MET A:207 , TYR A:210 , ALA A:242 , TRP A:243 , SER A:370 , GLU A:458BINDING SITE FOR RESIDUE GLC A1722
2AC2SOFTWAREARG A:340 , TYR A:592BINDING SITE FOR RESIDUE BR A1723
3AC3SOFTWARESER A:456 , GLY A:500 , SER A:501BINDING SITE FOR RESIDUE BR A1724
4AC4SOFTWAREASN A:121 , ILE A:122 , ALA A:167 , ASN A:169 , TYR A:190BINDING SITE FOR RESIDUE BR A1725
5AC5SOFTWARETHR A:558 , VAL A:571 , HOH A:2320BINDING SITE FOR RESIDUE BR A1726

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X42)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Asp A:58 -Gly A:59
2Ala A:117 -Pro A:118
3Lys A:163 -His A:164
4Phe A:165 -Val A:166
5Met A:261 -Pro A:262
6Leu A:345 -Pro A:346
7Phe A:559 -Pro A:560
8Glu A:562 -Pro A:563

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X42)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X42)

(-) Exons   (0, 0)

(no "Exon" information available for 2X42)

(-) 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:715
 aligned with Q0GC07_THENN | Q0GC07 from UniProtKB/TrEMBL  Length:721

    Alignment length:720
                                    11        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       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721
         Q0GC07_THENN     2 EKVNEILSQLTLEEKVKLVVGVGLPGLFGNPHSRVAGAAGETHPVPRVGLPAFVLADGPAGLRINPTRENDENTYYTTAFPVEIMLASTWNRELLEEVGKAMGEEVREYGVDVLLAPAMNIHRNPLCGRNFEYYSEDPVLSGEMASSFVKGVQSQGVGACIKHFVANNQETNRMVVDTIVSERALREIYLRGFEIAVKKSKPWSVMSAYNKLNGKYCSQNEWLLKKVLREEWGFEGFVMSDWYAGDNPVEQLKAGNDLIMPGKAYQVNTERRDEIEEIMEALKEGKLSEEVLDECVRNILKVLVNAPSFKNYRYSNKPDLEKHAKVAYEAGAEGVVLLRNEEALPLSENSKIALFGTGQIETIKGGTGSGDTHPRYAISILEGIKERGLNFDEELAKTYEDYIKKMRETEEYKPRRDSWGTIIKPKLPENFLSEKEIHKLAKKNDVAVIVISRISGEGYDRKPVKGDFYLSDDETDLIKTVSREFHEQGKKVIVLLNIGSPVEVVSWRDLVDGILLVWQAGQETGRIVADVLTGRINPSGKLPTTFPRDYSDVPSWTFPGEPKDNPQKVVYEEDIYVGYRYYDTFGVEPAYEFGYGLSYTTFEYSDLNVSFDGETLRVQYRIENTGGRAGKEVSQVYIKAPKGKIDKPFQELKAFHKTRLLNPGESEEVVLEIPVRDLASFNGEEWVVEAGEYEVRVGASSRNIKLKGTFSVGEERRFKP 721
               SCOP domains d2x42a1 A:2-319 Beta-glucosidase                                                                                                                                                                                                                                                                                              d2x42a2 A:320-599 Beta-glucosidase middle domain                                                                                                                                                                                                                                        d2x42a3 A:600-721 Beta-glucosidase C-terminal domain                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains Glyco_hydro_3-2x42A01 A:2-303                                                                                                                                                                                                                                                                                 --------------------------------Glyco_hydro_3_C-2x42A03 A:336-602                                                                                                                                                                                                                                          ------------------------------Fn3-like-2x42A02 A:633-702                                            ------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....................ee....hhhh....eee.........................hhhhhhhh.hhhhhhhhhhhhhhhhhhh...ee..............hhhhh...hhhhhhhhhhhhhhhhhh.....eeeee............eee.hhhhhhhhhhhhhhhhhhhhh..eeee...ee..ee...hhhhhhhhhhhhh....eeee......hhhhhhhhh.......hhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..eeeee...........eeeehhhhh..................hhhhhhhhh....hhhhhhhhhhhhhhhhhh.......-----...........hhhhhhhhhhhh.eeeeeee..................hhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhh.eeee...hhhhhhhhhhhhhh............ee.hhhhh..............eee.......hhhhhhhhh..eee..........eeeeeeeeee...eeeeeeeeee........eeeeeee...........eeeeeee........eeeeeeeee.hhhhee....eee..eeeeeeeeee..eeeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x42 A   2 EKVNEILSQLTLEEKVKLVVGVGLPGLFGNPHSRVAGAAGETHPVPRVGLPAFVLADGPAGLRINPTRENDENTYYTTAFPVEIMLASTWNRELLEEVGKAMGEEVREYGVDVLLAPAMNIHRNPLCGRNFEYYSEDPVLSGEMASSFVKGVQSQGVGACIKHFVANNQETNRMVVDTIVSERALREIYLRGFEIAVKKSKPWSVMSAYNKLNGKYCSQNEWLLKKVLREEWGFEGFVMSAWYAGDNPVEQLKAGNDLIMPGKAYQVNTERRDEIEEIMEALKEGKLSEEVLDECVRNILKVLVNAPSFKNYRYSNKPDLEKHAKVAYEAGAEGVVLLRNEEALPLSENSKIALFGTGQIETIKGGTGSGDTHPRYAISILEGIKERGLNFDEELAKTYEDYIKKMRETEEYKPRR-----IIKPKLPENFLSEKEIHKLAKKNDVAVIVISRISGEGYDRKPVKGDFYLSDDETDLIKTVSREFHEQGKKVIVLLNIGSPVEVVSWRDLVDGILLVWQAGQETGRIVADVLTGRINPSGKLPTTFPRDYSDVPSWTFPGEPKDNPQKVVYEEDIYVGYRYYDTFGVEPAYEFGYGLSYTTFEYSDLNVSFDGETLRVQYRIENTGGRAGKEVSQVYIKAPKGKIDKPFQELKAFHKTRLLNPGESEEVVLEIPVRDLASFNGEEWVVEAGEYEVRVGASSRNIKLKGTFSVGEERRFKP 721
                                    11        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     |   - |     431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721
                                                                                                                                                                                                                                                                                                                                                                                                                                                         417   423
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X42)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)
(-)
Clan: no clan defined [family: Fn3-like] (3)
(-)
Clan: no clan defined [family: Glyco_hydro_3_C] (3)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q0GC07_THENN | Q0GC07)
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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 Related Entries

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

UniProtKB/TrEMBL
        Q0GC07_THENN | Q0GC07: 2x40 2x41

(-) Related Entries Specified in the PDB File

2wt3 STRUCTURAL OF BETA-GLUCOSIDASE 3B FROM THERMOTOGA NEAPOLITANA IN COMPLEX WITH GLUCOSE : A THERMOSTABLE 3-DOMAIN REPRESENTATIVE OF GLYCOSIDE HYDROLASE FAMILY 3
2wt5 STRUCTURAL OF BETA-GLUCOSIDASE 3B FROM THERMOTOGA NEAPOLITANA IN COMPLEX WITH ALPHA- D-GLUCOSE
2wt6 STRUCTURAL OF BETA-GLUCOSIDASE 3B FROM THERMOTOGA NEAPOLITANA IN COMPLEX WITH GLYCEROL
2x40 STRUCTURE OF BETA-GLUCOSIDASE 3B FROM THERMOTOGA NEAPOLITANA IN COMPLEX WITH GLYCEROL
2x41 STRUCTURE OF BETA-GLUCOSIDASE 3B FROM THERMOTOGA NEAPOLITANA IN COMPLEX WITH GLUCOSE