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(-) Description

Title :  CRYSTAL STRUCTURE OF DEXTRAN GLUCOSIDASE E236Q COMPLEX WITH ISOMALTOTRIOSE
 
Authors :  H. Hondoh, W. Saburi, H. Mori, M. Okuyama, T. Nakada, Y. Matsuura, A. Kimura
Date :  14 Feb 08  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Barrel, (Beta/Alpha)8-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hondoh, W. Saburi, H. Mori, M. Okuyama, T. Nakada, Y. Matsuura, A. Kimura
Substrate Recognition Mechanism Of Alpha-1, 6-Glucosidic Linkage Hydrolyzing Enzyme, Dextran Glucosidase From Streptococcus Mutans.
J. Mol. Biol. V. 378 911 2008
PubMed-ID: 18395742  |  Reference-DOI: 10.1016/J.JMB.2008.03.016
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEXTRAN GLUCOSIDASE
    Chains: A
    EC Number: 3.2.1.70
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-23D
    Expression System Strain: BL21(DE3) CODONPLUS RIL
    Expression System Vector Type: PLASMID
    Gene: DEXB
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS MUTANS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2GLC3Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:60 , TYR A:63 , HIS A:103 , PHE A:139 , PHE A:158 , ARG A:192 , ASP A:194 , GLN A:236 , HIS A:312 , ASP A:313 , ARG A:398 , HOH A:983BINDING SITE FOR RESIDUE GLC A 877
2AC2SOFTWAREPHE A:139 , GLN A:236 , TRP A:238 , LYS A:275 , ASP A:313 , GLU A:371 , ARG A:398 , HOH A:1150BINDING SITE FOR RESIDUE GLC A 878
3AC3SOFTWARETRP A:238 , HOH A:1150BINDING SITE FOR RESIDUE GLC A 879
4AC4SOFTWAREASP A:148 , ASP A:151 , GLU A:508BINDING SITE FOR RESIDUE CA A 880
5AC5SOFTWARETHR A:417 , GLU A:516 , HOH A:1066 , HOH A:1077 , HOH A:1159 , HOH A:1160 , HOH A:1161BINDING SITE FOR RESIDUE CA A 881
6AC6SOFTWAREASP A:21 , ASN A:23 , ASP A:25 , ILE A:27 , ASP A:29BINDING SITE FOR RESIDUE CA A 882

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZID)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZID)

(-) 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:536
 aligned with DEXB_STRMU | Q99040 from UniProtKB/Swiss-Prot  Length:536

    Alignment length:536
                                    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      
           DEXB_STRMU     1 MQKHWWHKATVYQIYPKSFMDTNGDGIGDLKGITSKLDYLQKLGVMAIWLSPVYDSPMDDNGYDIANYEAITDIFGNMADMDNLLTQAKMRGIKIIMDLVVNHTSDEHAWFIEAREHPDSSERDYYIWCDQPNDLESIFGGSAWQYDDKSDQYYLHFFSKKQPDLNWENANLRQKIYDMMNFWIDKGIGGFRMDVIDMIGKIPAQHIVSNGPKLHAYLKEMNAASFGQHDLLTVGETWGATPEIAKQYSNPVNHELSMVFQFEHIGLQHKPEAPKWDYVKELNVPALKTIFNKWQTELELGQGWNSLFWNNHDLPRVLSIWGNTGKYREKSAKALAILLHLMRGTPYIYQGEEIGMTNYPFKDLNELDDIESLNYAKEAFTNGKSMETIMDSIRMIGRDNARTPMQWDASQNAGFSTADKTWLPVNPNYKDINVQAALKNSNSIFYTYQQLIQLRKENDWLVDADFELLPTADKVFAYLRKVREERYLIVVNVSDQEEVLEIDVDKQETLISNTNESAALANHKLQPWDAFCIKIN 536
               SCOP domains d2zida1 A:1-463 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                              d2zida2 A:464-536 automated matches                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------Alpha-amylase-2zidA01 A:28-363                                                                                                                                                                                                                                                                                                                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.eeeehhhhh.........hhhhhhhhhhhhhhhh..eeee...ee...........eeeee.hhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhh..hhhhhhh.ee..............eeee....eeee.............hhhhhhhhhhhhhhhhh....eeee.hhhhh..hhhhh......hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eee...hhhhhh.............hhhhhhhhhhhhhhhh.......ee........hhhhhhh....hhhhhhhhhhhhhhh...eeeee.hhhhh.......hhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhh..........hhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhheeee......eeeeeeee..eeeeeeee.....ee......eeeeeee..hhhhhhhhhee....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zid A   1 MQKHWWHKATVYQIYPKSFMDTNGDGIGDLKGITSKLDYLQKLGVMAIWLSPVYDSPMDDNGYDIANYEAIADIFGNMADMDNLLTQAKMRGIKIIMDLVVNHTSDEHAWFIEAREHPDSSERDYYIWCDQPNDLESIFGGSAWQYDDKSDQYYLHFFSKKQPDLNWENANLRQKIYDMMNFWIDKGIGGFRMDVIDMIGKIPAQHIVSNGPKLHAYLKEMNAASFGQHDLLTVGQTWGATPEIAKQYSNPVNHELSMVFQFEHIGLQHKPEAPKWDYVKELNVPALKTIFNKWQTELELGQGWNSLFWNNHDLPRVLSIWGNTGKYREKSAKALAILLHLMRGTPYIYQGEEIGMTNYPFKDLNELDDIESLNYAKEAFTNGKSMETIMDSIRMIGRDNARTPMQWDASQNAGFSTADKTWLPVNPNYKDINVQAALKNSNSIFYTYQQLIQLRKENDWLVDADFELLPTADKVFAYLRKVREERYLIVVNVSDQEEVLEIDVDKQETLISNTNESAALANHKLQPWDAFCIKIL 536
                                    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      


Chain A from PDB  Type:PROTEIN  Length:536
 aligned with Q2HWU5_STRMG | Q2HWU5 from UniProtKB/TrEMBL  Length:531

    Alignment length:536
                                 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525      
         Q2HWU5_STRMG     - -----WHKATVYQIYPKSFMDTNGDGIGDLKGITSKLDYLQKLGVMAIWLSPVYDSPMDDNGYDIANYEAIADIFGNMADMDNLLTQAKMRGIKIIMDLVVNHTSDEHAWFIEAREHPDSSERDYYIWCDQPNDLESIFGGSAWQYDDKSDQYYLHFFSKKQPDLNWENANLRQKIYDMMNFWIDKGIGGFRMDVIDMIGKIPAQHIVSNGPKLHAYLKEMNAASFGQHDLLTVGETWGATPEIAKQYSNPVNHELSMVFQFEHIGLQHKPEAPKWDYVKELNVPALKTIFNKWQTELELGQGWNSLFWNNHDLPRVLSIWGNTGKYREKSAKALAILLHLMRGTPYIYQGEEIGMTNYPFKDLNELDDIESLNYAKEAFTNGKSMETIMDSIRMIGRDNARTPMQWDASQNAGFSTADKTWLPVNPNYKDINVQAALKNSNSIFYTYQQLIQLRKENDWLVDADFELLPTADKVFAYLRKVREERYLIVVNVSDQEEVLEIDVDKQETLISNTNESAALANHKLQPWDAFCIKIN 531
               SCOP domains d2zida1 A:1-463 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                              d2zida2 A:464-536 automated matches                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------Alpha-amylase-2zidA01 A:28-363                                                                                                                                                                                                                                                                                                                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.eeeehhhhh.........hhhhhhhhhhhhhhhh..eeee...ee...........eeeee.hhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhh..hhhhhhh.ee..............eeee....eeee.............hhhhhhhhhhhhhhhhh....eeee.hhhhh..hhhhh......hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eee...hhhhhh.............hhhhhhhhhhhhhhhh.......ee........hhhhhhh....hhhhhhhhhhhhhhh...eeeee.hhhhh.......hhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhh..........hhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhheeee......eeeeeeee..eeeeeeee.....ee......eeeeeee..hhhhhhhhhee....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zid A   1 MQKHWWHKATVYQIYPKSFMDTNGDGIGDLKGITSKLDYLQKLGVMAIWLSPVYDSPMDDNGYDIANYEAIADIFGNMADMDNLLTQAKMRGIKIIMDLVVNHTSDEHAWFIEAREHPDSSERDYYIWCDQPNDLESIFGGSAWQYDDKSDQYYLHFFSKKQPDLNWENANLRQKIYDMMNFWIDKGIGGFRMDVIDMIGKIPAQHIVSNGPKLHAYLKEMNAASFGQHDLLTVGQTWGATPEIAKQYSNPVNHELSMVFQFEHIGLQHKPEAPKWDYVKELNVPALKTIFNKWQTELELGQGWNSLFWNNHDLPRVLSIWGNTGKYREKSAKALAILLHLMRGTPYIYQGEEIGMTNYPFKDLNELDDIESLNYAKEAFTNGKSMETIMDSIRMIGRDNARTPMQWDASQNAGFSTADKTWLPVNPNYKDINVQAALKNSNSIFYTYQQLIQLRKENDWLVDADFELLPTADKVFAYLRKVREERYLIVVNVSDQEEVLEIDVDKQETLISNTNESAALANHKLQPWDAFCIKIL 536
                                    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
   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  (0, 0)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (7, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DEXB_STRMU | Q99040)
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.
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.

Chain A   (Q2HWU5_STRMG | Q2HWU5)
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.
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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  2zid
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 Related Entries

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

UniProtKB/Swiss-Prot
        DEXB_STRMU | Q99040: 2zic 4wlc 4xb3
        Q2HWU5_STRMG | Q2HWU5: 2zic

(-) Related Entries Specified in the PDB File

2zic