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(-) Description

Title :  BETA-GLYCOSIDASE FROM PYROCOCCUS HORIKOSHII
 
Authors :  T. Akiba, M. Nishio, I. Matsui, K. Harata
Date :  12 Apr 04  (Deposition) - 29 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosyl Hydrolase, Membrane-Bound Enzyme, Thermostability, Tim Barrel, Alkylglucosides (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Akiba, M. Nishio, I. Matsui, K. Harata
X-Ray Structure Of A Membrane-Bound Beta-Glycosidase From The Hyperthermophilic Archaeon Pyrococcus Horikoshii
Proteins V. 57 422 2004
PubMed-ID: 15340929  |  Reference-DOI: 10.1002/PROT.20203
(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 BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PH0366
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: BETA-GLYCOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VFF)

(-) Sites  (0, 0)

(no "Site" information available for 1VFF)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VFF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:38 -Pro A:39
2Pro A:170 -Pro A:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VFF)

(-) 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:423
 aligned with O58104_PYRHO | O58104 from UniProtKB/TrEMBL  Length:423

    Alignment length:423
                                    10        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   
         O58104_PYRHO     1 MPLKFPEMFLFGTATSSHQIEGNNRWNDWWYYEQIGKLPYRSGKACNHWELYRDDIQLMTSLGYNAYRFSIEWSRLFPEENKFNEDAFMKYREIIDLLLTRGITPLVTLHHFTSPLWFMKKGGFLREENLKHWEKYIEKVAELLEKVKLVATFNEPMVYVMMGYLTAYWPPFIRSPFKAFKVAANLLKAHAIAYELLHGKFKVGIVKNIPIILPASDKERDRKAAEKADNLFNWHFLDAIWSGKYRGVFKTYRIPQSDADFIGVNYYTASEVRHTWNPLKFFFEVKLADISERKTQMGWSVYPKGIYMALKKASRYGRPLYITENGIATLDDEWRVEFIIQHLQYVHKAIEDGLDVRGYFYWSFMDNYEWKEGFGPRFGLVEVDYQTFERRPRKSAYVYGEIARSKEIKDELLKRYGLPELQL 423
               SCOP domains d1vffa1 A:1-423 Beta-glucosidase A                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1vffA00 A:1-423 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains Glyco_hydro_1-1vffA01 A:1-408                                                                                                                                                                                                                                                                                                                                                                                           --------------- Pfam domains
         Sec.struct. author ..ee.....eeeee............hhhhhhhhh...........hhhhhhhhhhhhhhhhh..eeeee.hhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhheee....eee........eeee...eeeeee..hhhhh.eeeee...............hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh.......eee......eeehhhhhhhhhhhhhheehhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vff A   1 MPLKFPEMFLFGTATSSHQIEGNNRWNDWWYYEQIGKLPYRSGKACNHWELYRDDIQLMTSLGYNAYRFSIEWSRLFPEENKFNEDAFMKYREIIDLLLTRGITPLVTLHHFTSPLWFMKKGGFLREENLKHWEKYIEKVAELLEKVKLVATFNEPMVYVMMGYLTAYWPPFIRSPFKAFKVAANLLKAHAIAYELLHGKFKVGIVKNIPIILPASDKERDRKAAEKADNLFNWHFLDAIWSGKYRGVFKTYRIPQSDADFIGVNYYTASEVRHTWNPLKFFFEVKLADISERKTQMGWSVYPKGIYMALKKASRYGRPLYITENGIATLDDEWRVEFIIQHLQYVHKAIEDGLDVRGYFYWSFMDNYEWKEGFGPRFGLVEVDYQTFERRPRKSAYVYGEIARSKEIKDELLKRYGLPELQL 423
                                    10        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
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O58104_PYRHO | O58104)
molecular function
    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.

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  Cis Peptide Bonds
    Leu A:38 - Pro A:39   [ RasMol ]  
    Pro A:170 - Pro A:171   [ RasMol ]  
 

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