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(-) Description

Title :  CRYSTAL STRUCTURE OF B. CEREUS OLIGO-1,6-GLUCOSIDASE
 
Authors :  K. Watanabe, Y. Hata, H. Kizaki, Y. Katsube, Y. Suzuki
Date :  28 Jul 98  (Deposition) - 16 Feb 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Glucosidase, Sugar Degradation, Hydrolase, Tim-Barrel Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Watanabe, Y. Hata, H. Kizaki, Y. Katsube, Y. Suzuki
The Refined Crystal Structure Of Bacillus Cereus Oligo-1, 6-Glucosidase At 2. 0 A Resolution: Structural Characterization Of Proline-Substitution Sites For Protein Thermostabilization.
J. Mol. Biol. V. 269 142 1997
PubMed-ID: 9193006  |  Reference-DOI: 10.1006/JMBI.1997.1018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OLIGO-1,6-GLUCOSIDASE
    Atcc: ATCC 7064
    Chains: A
    Collection: ATCC 7064
    EC Number: 3.2.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBCE4-2
    Expression System Strain: MV1184
    Expression System Taxid: 562
    Expression System Vector: PUC118
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396

 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 1UOK)

(-) Sites  (0, 0)

(no "Site" information available for 1UOK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:540 -Pro A:541

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UOK)

(-) 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:558
 aligned with O16G_BACCE | P21332 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:558
                                    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       490       500       510       520       530       540       550        
           O16G_BACCE     1 MEKQWWKESVVYQIYPRSFMDSNGDGIGDLRGIISKLDYLKELGIDVIWLSPVYESPNDDNGYDISDYCKIMNEFGTMEDWDELLHEMHERNMKLMMDLVVNHTSDEHNWFIESRKSKDNKYRDYYIWRPGKEGKEPNNWGAAFSGSAWQYDEMTDEYYLHLFSKKQPDLNWDNEKVRQDVYEMMKFWLEKGIDGFRMDVINFISKEEGLPTVETEEEGYVSGHKHFMNGPNIHKYLHEMNEEVLSHYDIMTVGEMPGVTTEEAKLYTGEERKELQMVFQFEHMDLDSGEGGKWDVKPCSLLTLKENLTKWQKALEHTGWNSLYWNNHDQPRVVSRFGNDGMYRIESAKMLATVLHMMKGTPYIYQGEEIGMTNVRFESIDEYRDIETLNMYKEKVMERGEDIEKVMQSIYIKGRDNARTPMQWDDQNHAGFTTGEPWITVNPNYKEINVKQAIQNKDSIFYYYKKLIELRKNNEIVVYGSYDLILENNPSIFAYVRTYGVEKLLVIANFTAEECIFELPEDISYSEVELLIHNYDVENGPIENITLRPYEAMVFKLK 558
               SCOP domains d1uoka2 A:1-479 Oligo-1,6, glucosidase                                                                                                                                                                                                                                                                                                                                                                                                                                                         d1uoka1 A:480-558 Oligo-1,6-glucosidase                                         SCOP domains
               CATH domains 1uokA01 A:1-104,A:175-480 Glycosidases                                                                  1uokA02 A:105-174 Oligo-1,6-glucosidase; Domain 2                     1uokA01 A:1-104,A:175-480 Glycosidases                                                                                                                                                                                                                                                                            1uokA03 A:481-558 Golgi alpha-mannosidase II                                   CATH domains
               Pfam domains ---------------------------Alpha-amylase-1uokA01 A:28-385                                                                                                                                                                                                                                                                                                                                        ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheeeeeeehhh...........hhhhhhhhhhhhhh...eeee......................hhh..hhhhhhhhhhhhh..eeeeeeee........hhhhhh........hhh.eeeee.................eeee....eeee..............hhhhhhhhhhhhhhhh....eeee..hhh....................hhh......hhhhhhhhhhh.hhh..eeeeeee....hhhhhhhh.hhh....eeee.hhhhh..............hhhhhhhhhhhhhh.....eeeee........hhhhh......hhhhhhhhhhhhh....eeeee..hhh.........hhh...hhhhhhhhhhhh.....hhhhhhhhhhh.hhhh........................hhhh...hhhhhh....hhhhhhhhhhhhhh.hhhhh.eeeee......eeeeeeee..eeeeeeee.....eeee........eeeeeee..eeeee...eeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1uok A   1 MEKQWWKESVVYQIYPRSFMDSNGDGIGDLRGIISKLDYLKELGIDVIWLSPVYESPNDDNGYDISDYCKIMNEFGTMEDWDELLHEMHERNMKLMMDLVVNHTSDEHNWFIESRKSKDNKYRDYYIWRPGKEGKEPNNWGAAFSGSAWQYDEMTDEYYLHLFSKKQPDLNWDNEKVRQDVYEMMKFWLEKGIDGFRMDVINFISKEEGLPTVETEEEGYVSGHKHFMNGPNIHKYLHEMNEEVLSHYDIMTVGEMPGVTTEEAKLYTGEERKELQMVFQFEHMDLDSGEGGKWDVKPCSLLTLKENLTKWQKALEHTGWNSLYWNNHDQPRVVSRFGNDGMYRIESAKMLATVLHMMKGTPYIYQGEEIGMTNVRFESIDEYRDIETLNMYKEKVMERGEDIEKVMQSIYIKGRDNARTPMQWDDQNHAGFTTGEPWITVNPNYKEINVKQAIQNKDSIFYYYKKLIELRKNNEIVVYGSYDLILENNPSIFAYVRTYGVEKLLVIANFTAEECIFELPEDISYSEVELLIHNYDVENGPIENITLRPYEAMVFKLK 558
                                    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       490       500       510       520       530       540       550
   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  (2, 2)

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

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O16G_BACCE | P21332)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004574    oligo-1,6-glucosidase activity    Catalysis of the hydrolysis of (1->6)-alpha-D-glucosidic linkages in some oligosaccharides produced from starch and glycogen by alpha-amylase, and in isomaltose. Releases a free alpha-D-glucose.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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    Gly A:540 - Pro A:541   [ RasMol ]  
 

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