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(-) Description

Title :  STRUCTURE OF GLUCAN-1,6-ALPHA-GLUCOSIDASE FROM LACTOBACILLUS ACIDOPHILUS NCFM
 
Authors :  F. Fredslund, J. C. Navarro Poulsen, L. Lo Leggio
Date :  09 Feb 12  (Deposition) - 29 Aug 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Glycoside Hydrolase 13 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Moller, F. Fredslund, A. Majumder, H. Nakai, J. N. Poulsen, L. Lo Leggio, B. Svensson, M. Abou Hachem
Enzymology And Structure Of The Gh13_31 Glucan 1, 6-Alpha- Glucosidase That Confers Isomaltooligosaccharide Utilization In The Probiotic Lactobacillus Acidophilus Ncfm.
J. Bacteriol. V. 194 4249 2012
PubMed-ID: 22685275  |  Reference-DOI: 10.1128/JB.00622-12

(-) Compounds

Molecule 1 - GLUCAN 1,6-ALPHA-GLUCOSIDASE
    Atcc: 700396
    Chains: A
    EC Number: 3.2.1.70, 3.2.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET21A
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2-539
    Organism Scientific: LACTOBACILLUS ACIDOPHILUS NCFM
    Organism Taxid: 272621
    Synonym: ALPHA-GLUCOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL8Ligand/IonGLYCEROL
3MES3Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:41 , TYR A:330 , GLN A:451 , ASN A:498 , GLU A:499 , GLU A:500 , PRO A:529 , HOH A:2186 , HOH A:2455BINDING SITE FOR RESIDUE MES A1539
02AC2SOFTWAREASP A:20 , ASN A:22 , ASP A:24 , ILE A:26 , ASP A:28 , HOH A:2030BINDING SITE FOR RESIDUE CA A1540
03AC3SOFTWARELYS A:93 , GLY A:191 , ILE A:192 , ARG A:233 , ASP A:234 , ASP A:388 , GLU A:390BINDING SITE FOR RESIDUE GOL A1541
04AC4SOFTWAREASP A:59 , TYR A:62 , HIS A:102 , PHE A:143 , ASP A:198 , ARG A:401 , HOH A:2215 , HOH A:2249 , HOH A:2334BINDING SITE FOR RESIDUE GOL A1542
05AC5SOFTWAREASP A:66 , GLU A:68 , HIS A:107 , LYS A:108 , PRO A:130 , GLU A:133 , TYR A:150 , TYR A:157 , HOH A:2076 , HOH A:2078 , HOH A:2185BINDING SITE FOR RESIDUE MES A1543
06AC6SOFTWARESER A:322 , ARG A:323 , ASN A:361 , HOH A:2341 , HOH A:2366BINDING SITE FOR RESIDUE GOL A1544
07AC7SOFTWAREASP A:20 , GLY A:23 , GLY A:417 , PHE A:418 , SER A:419 , GLU A:420BINDING SITE FOR RESIDUE GOL A1545
08AC8SOFTWARELYS A:117 , ASP A:129 , SER A:154 , GLN A:156 , PHE A:186 , HOH A:2211 , HOH A:2474BINDING SITE FOR RESIDUE GOL A1546
09AC9SOFTWARESER A:34 , ARG A:35 , ASP A:37 , TYR A:38 , HOH A:2046 , HOH A:2475BINDING SITE FOR RESIDUE MES A1547
10BC1SOFTWARELYS A:279 , ASP A:316 , GLU A:374 , ARG A:401 , GOL A:1549 , HOH A:2249BINDING SITE FOR RESIDUE GOL A1548
11BC2SOFTWAREPHE A:162 , VAL A:199 , GLU A:201 , LEU A:202 , ARG A:212 , TRP A:242 , GOL A:1548 , HOH A:2218 , HOH A:2226 , HOH A:2249BINDING SITE FOR RESIDUE GOL A1549
12BC3SOFTWAREASP A:118 , ILE A:376 , TYR A:379 , ASN A:380 , HOH A:2374BINDING SITE FOR RESIDUE GOL A1550

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AIE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AIE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AIE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AIE)

(-) Exons   (0, 0)

(no "Exon" information available for 4AIE)

(-) 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:537
 aligned with Q5FMB7_LACAC | Q5FMB7 from UniProtKB/TrEMBL  Length:539

    Alignment length:537
                                    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       
         Q5FMB7_LACAC     2 ASWWKNAVVYQVYPKSFQDSNGDGIGDLQGIISRLDYLEKLGIDAIWLSPVYQSPGVDNGYDISDYEAIDPQYGTMADMDELISKAKEHHIKIVMDLVVNHTSDQHKWFVEAKKGKDNQYRDYYIWRDPVDEHEPNDLKSAFSGSAWKYDERSGQYYLHFFADQQPDLNWQNTELRQKIYNMMNFWLDKGIGGFRMDVIELIGKDPDKNIRENGPMLHPYLQEMNKATFGKRDVMTVGETWNATPKIAEEYSDPDRHELSMVFQFENQSLDQQPGKEKWDLKPLDLGELKKVLVKWQTKIDFDHAWNSLFWENHDIPRVISRWGNDQEYRVQCAKMFAIILHMMHGTPYIFNGEEIGMTNCPVKNIDEVEDIESINMYNERLAEGYDEEELIHAINVKGRDNARRPMQWNDEKNAGFSEVDPWLSVNPNYKDINVENALADPNSIFYTYQKLIKLRHENPIVVDGDFSLVSNTQDAVLAYYRILNDKKWLVVANLSNEEQNFVSNDQIETILSNYPERNNVQNITLKPYEAFISKVI 538
               SCOP domains d4aiea1 A:2-465 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                               d4aiea2 A:466-538 automated matches                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhh.........hhhhhhhhhhhhhhhh..eeee...ee...........eeeee.....hhhhhhhhhhhhhhh..eeeeee........hhhhhhhh......hhhh..ee...................eeee....eeee.............hhhhhhhhhhhhhhhhhh...eeee.hhhhh.............hhhhhhhhhhhhh......eeeee....hhhhhhhh..hhh....eee.hhhhhhh.............hhhhhhhhhhhhhhh........ee........hhhhhhh....hhhhhhhhhhhhhhh...eeeee.hhhhh.......hhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhh......................hhhhhh.hhhhhhhh..hhhhhhhhhhhhhhh.hhhhh.eeee.......eeeeeeee..eeeeeeee.....eeee...eeeeeee.........eeee....eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aie A   2 ASWWKNAVVYQVYPKSFQDSNGDGIGDLQGIISRLDYLEKLGIDAIWLSPVYQSPGVDNGYDISDYEAIDPQYGTMADMDELISKAKEHHIKIVMDLVVNHTSDQHKWFVEAKKGKDNQYRDYYIWRDPVDEHEPNDLKSAFSGSAWKYDERSGQYYLHFFADQQPDLNWQNTELRQKIYNMMNFWLDKGIGGFRMDVIELIGKDPDKNIRENGPMLHPYLQEMNKATFGKRDVMTVGETWNATPKIAEEYSDPDRHELSMVFQFENQSLDQQPGKEKWDLKPLDLGELKKVLVKWQTKIDFDHAWNSLFWENHDIPRVISRWGNDQEYRVQCAKMFAIILHMMHGTPYIFNGEEIGMTNCPVKNIDEVEDIESINMYNERLAEGYDEEELIHAINVKGRDNARRPMQWNDEKNAGFSEVDPWLSVNPNYKDINVENALADPNSIFYTYQKLIKLRHENPIVVDGDFSLVSNTQDAVLAYYRILNDKKWLVVANLSNEEQNFVSNDQIETILSNYPERNNVQNITLKPYEAFISKVI 538
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "CATH Domain" information available for 4AIE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AIE)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5FMB7_LACAC | Q5FMB7)
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:0043896    glucan 1,6-alpha-glucosidase activity    Catalysis of the hydrolysis of (1->6)-alpha-D-glucosidic linkages in (1->6)-alpha-D-glucans and derived oligosaccharides.
    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.
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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