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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BETA-GLYCOSIDASE FROM THE HYPERTHERMOPHILE THERMOSPHAERA AGGREGANS
 
Authors :  Y. -I. Chi, L. A. Martinez-Cruz, R. V. Swanson, D. E. Robertson, S. - H. Kim
Date :  07 Jul 99  (Deposition) - 13 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Tim-Barrel, Thermostable, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. I. Chi, L. A. Martinez-Cruz, J. Jancarik, R. V. Swanson, D. E. Robertson, S. H. Kim
Crystal Structure Of The Beta-Glycosidase From The Hyperthermophile Thermosphaera Aggregans: Insights Into Its Activity And Thermostability.
Febs Lett. V. 445 375 1999
PubMed-ID: 10094493  |  Reference-DOI: 10.1016/S0014-5793(99)00090-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-GLYCOSIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Taxid: 562
    Organism Scientific: THERMOSPHAERA AGGREGANS
    Organism Taxid: 54254

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1QVB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:225 -Pro A:226
2Pro B:225 -Pro B:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QVB)

(-) 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:481
 aligned with Q9YGA8_9CREN | Q9YGA8 from UniProtKB/TrEMBL  Length:481

    Alignment length:481
                                    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       430       440       450       460       470       480 
         Q9YGA8_9CREN     1 MKFPKDFMIGYSSSPFQFEAGIPGSEDPNSDWWVWVHDPENTAAGLVSGDFPENGPGYWNLNQNDHDLAEKLGVNTIRVGVEWSRIFPKPTFNVKVPVERDENGSIVHVDVDDKAVERLDELANKEAVNHYVEMYKDWVERGRKLILNLYHWPLPLWLHNPIMVRRMGPDRAPSGWLNEESVVEFAKYAAYIAWKMGELPVMWSTMNEPNVVYEQGYMFVKGGFPPGYLSLEAADKARRNMIQAHARAYDNIKRFSKKPVGLIYAFQWFELLEGPAEVFDKFKSSKLYYFTDIVSKGSSIINVEYRRDLANRLDWLGVNYYSRLVYKIVDDKPIILHGYGFLCTPGGISPAENPCSDFGWEVYPEGLYLLLKELYNRYGVDLIVTENGVSDSRDALRPAYLVSHVYSVWKAANEGIPVKGYLHWSLTDNYEWAQGFRQKFGLVMVDFKTKKRYLRPSALVFREIATHNGIPDELQHLTLIQ 481
               SCOP domains d1qvba_ A: beta-Glycosidase                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1qvbA00 A:1-481 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.hhhhhh..........hhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhh..........eee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eee......hhhhhhhhhhh....hhhhhh.................eeeee...eeeee......ee...hhhhh....................hhhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh.......eeee....eeeehhhhhhhhhhhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qvb A   1 MKFPKDFMIGYSSSPFQFEAGIPGSEDPNSDWWVWVHDPENTAAGLVSGDFPENGPGYWNLNQNDHDLAEKLGVNTIRVGVEWSRIFPKPTFNVKVPVERDENGSIVHVDVDDKAVERLDELANKEAVNHYVEMYKDWVERGRKLILNLYHWPLPLWLHNPIMVRRMGPDRAPSGWLNEESVVEFAKYAAYIAWKMGELPVMWSTMNEPNVVYEQGYMFVKGGFPPGYLSLEAADKARRNMIQAHARAYDNIKRFSKKPVGLIYAFQWFELLEGPAEVFDKFKSSKLYYFTDIVSKGSSIINVEYRRDLANRLDWLGVNYYSRLVYKIVDDKPIILHGYGFLCTPGGISPAENPCSDFGWEVYPEGLYLLLKELYNRYGVDLIVTENGVSDSRDALRPAYLVSHVYSVWKAANEGIPVKGYLHWSLTDNYEWAQGFRQKFGLVMVDFKTKKRYLRPSALVFREIATHNGIPDELQHLTLIQ 481
                                    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       430       440       450       460       470       480 


Chain B from PDB  Type:PROTEIN  Length:481
 aligned with Q9YGA8_9CREN | Q9YGA8 from UniProtKB/TrEMBL  Length:481

    Alignment length:481
                                    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       430       440       450       460       470       480 
         Q9YGA8_9CREN     1 MKFPKDFMIGYSSSPFQFEAGIPGSEDPNSDWWVWVHDPENTAAGLVSGDFPENGPGYWNLNQNDHDLAEKLGVNTIRVGVEWSRIFPKPTFNVKVPVERDENGSIVHVDVDDKAVERLDELANKEAVNHYVEMYKDWVERGRKLILNLYHWPLPLWLHNPIMVRRMGPDRAPSGWLNEESVVEFAKYAAYIAWKMGELPVMWSTMNEPNVVYEQGYMFVKGGFPPGYLSLEAADKARRNMIQAHARAYDNIKRFSKKPVGLIYAFQWFELLEGPAEVFDKFKSSKLYYFTDIVSKGSSIINVEYRRDLANRLDWLGVNYYSRLVYKIVDDKPIILHGYGFLCTPGGISPAENPCSDFGWEVYPEGLYLLLKELYNRYGVDLIVTENGVSDSRDALRPAYLVSHVYSVWKAANEGIPVKGYLHWSLTDNYEWAQGFRQKFGLVMVDFKTKKRYLRPSALVFREIATHNGIPDELQHLTLIQ 481
               SCOP domains d1qvbb_ B: beta-Glycosidase                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1qvbB00 B:1-481 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------Glyco_hydro_1-1qvbB01 B:120-470                                                                                                                                                                                                                                                                                                                                ----------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------Glyco_hydro_1-1qvbB02 B:120-470                                                                                                                                                                                                                                                                                                                                ----------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------Glyco_hydro_1-1qvbB03 B:120-470                                                                                                                                                                                                                                                                                                                                ----------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------Glyco_hydro_1-1qvbB04 B:120-470                                                                                                                                                                                                                                                                                                                                ----------- Pfam domains (4)
         Sec.struct. author .......eeeee.hhhhhh..........hhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhh..........eee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eee......hhhhhhhhhhh....hhhhhh.................eeeee...eeeee......ee...hhhhh....................hhhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh.......eeee....eeeehhhhhhhhhhhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qvb B   1 MKFPKDFMIGYSSSPFQFEAGIPGSEDPNSDWWVWVHDPENTAAGLVSGDFPENGPGYWNLNQNDHDLAEKLGVNTIRVGVEWSRIFPKPTFNVKVPVERDENGSIVHVDVDDKAVERLDELANKEAVNHYVEMYKDWVERGRKLILNLYHWPLPLWLHNPIMVRRMGPDRAPSGWLNEESVVEFAKYAAYIAWKMGELPVMWSTMNEPNVVYEQGYMFVKGGFPPGYLSLEAADKARRNMIQAHARAYDNIKRFSKKPVGLIYAFQWFELLEGPAEVFDKFKSSKLYYFTDIVSKGSSIINVEYRRDLANRLDWLGVNYYSRLVYKIVDDKPIILHGYGFLCTPGGISPAENPCSDFGWEVYPEGLYLLLKELYNRYGVDLIVTENGVSDSRDALRPAYLVSHVYSVWKAANEGIPVKGYLHWSLTDNYEWAQGFRQKFGLVMVDFKTKKRYLRPSALVFREIATHNGIPDELQHLTLIQ 481
                                    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       430       440       450       460       470       480
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9YGA8_9CREN | Q9YGA8)
molecular function
    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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