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(-) Description

Title :  CARBOHYDRATE-BINDING OF THE STARCH BINDING DOMAIN OF RHIZOPUS ORYZAE GLUCOAMYLASE IN COMPLEX WITH BETA-CYCLODEXTRIN AND MALTOHEPTAOSE
 
Authors :  J. -Y. Tung, Y. -Y. Liu, Y. -J. Sun
Date :  09 Aug 07  (Deposition) - 19 Aug 08  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Carbohydrate Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. -Y. Tung, M. D. -T. Chang, W. -I. Chou, Y. -Y. Liu, Y. Yeh, F. Chang, S. Lin, Z. Qiu, Y. -J. Sun
Crystal Structures Of The Starch-Binding Domain From Rhizopus Oryzae Glucoamylase Reveal A Polysaccharide-Binding Path.
Biochem. J. V. 416 27 2008
PubMed-ID: 18588504  |  Reference-DOI: 10.1042/BJ20080580

(-) Compounds

Molecule 1 - GLUCOAMYLASE A
    ChainsA
    EC Number3.2.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET23A
    Expression System Vector TypePLASMID
    FragmentSTARCH BINDING DOMAIN, RESIDUES 26-131
    Organism ScientificRHIZOPUS ORYZAE
    Organism Taxid64495

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1GLC7Ligand/IonALPHA-D-GLUCOSE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:1 , ASP A:12 , THR A:106 , HOH A:2016 , HOH A:2114 , HOH A:2115BINDING SITE FOR RESIDUE ZN A1107
2AC2SOFTWAREASN A:29 , TYR A:32 , SER A:33 , LYS A:34 , TRP A:47 , ASN A:50 , PHE A:58 , GLU A:68 , TRP A:70 , LYS A:77 , TYR A:83 , TYR A:94 , ASN A:96 , ASN A:101 , HOH A:2039 , HOH A:2044 , HOH A:2058 , HOH A:2102 , HOH A:2116 , HOH A:2117 , HOH A:2121 , HOH A:2122 , HOH A:2123 , HOH A:2124 , HOH A:2125BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1108 TO 1114

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V8L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V8L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V8L)

(-) Exons   (0, 0)

(no "Exon" information available for 2V8L)

(-) 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:106
 aligned with B7XC04_RHIOR | B7XC04 from UniProtKB/TrEMBL  Length:604

    Alignment length:106
                                    35        45        55        65        75        85        95       105       115       125      
         B7XC04_RHIOR    26 ASIPSSASVQLDSYNYDGSTFSGKIYVKNIAYSKKVTVVYADGSDNWNNNGNIIAASFSGPISGSNYEYWTFSASVKGIKEFYIKYEVSGKTYYDNNNSANYQVST 131
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeee...eeeeeeeee.....eeeeeee............eee.eeeee.....eeeeeeeee.....eeeeeeee..eeeee......ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2v8l A   1 ASIPSSASVQLDSYNYDGSTFSGKIYVKNIAYSKKVTVVYADGSDNWNNNGNIIAASFSGPISGSNYEYWTFSASVKGIKEFYIKYEVSGKTYYDNNNSANYQVST 106
                                    10        20        30        40        50        60        70        80        90       100      

Chain A from PDB  Type:PROTEIN  Length:106
 aligned with Q2VC81_RHIOR | Q2VC81 from UniProtKB/TrEMBL  Length:604

    Alignment length:106
                                    35        45        55        65        75        85        95       105       115       125      
         Q2VC81_RHIOR    26 ASIPSSASVQLDSYNYDGSTFSGKIYVKNIAYSKKVTVVYADGSDNWNNNGNTIAASFSGPISGSNYEYWTFSASVKGIKEFYIKYEVSGKTYYDNNNSANYQVST 131
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeee...eeeeeeeee.....eeeeeee............eee.eeeee.....eeeeeeeee.....eeeeeeee..eeeee......ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2v8l A   1 ASIPSSASVQLDSYNYDGSTFSGKIYVKNIAYSKKVTVVYADGSDNWNNNGNIIAASFSGPISGSNYEYWTFSASVKGIKEFYIKYEVSGKTYYDNNNSANYQVST 106
                                    10        20        30        40        50        60        70        80        90       100      

   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  (0, 0)

(no "SCOP Domain" information available for 2V8L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V8L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V8L)

(-) Gene Ontology  (4, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q2VC81_RHIOR | Q2VC81)
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:0004339    glucan 1,4-alpha-glucosidase activity    Catalysis of the hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose.
biological process
    GO:0005976    polysaccharide metabolic process    The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Chain A   (B7XC04_RHIOR | B7XC04)
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:0004339    glucan 1,4-alpha-glucosidase activity    Catalysis of the hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0005976    polysaccharide metabolic process    The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q2VC81_RHIOR | Q2VC812v8m
UniProtKB/TrEMBL
        B7XC04_RHIOR | B7XC042v8m 4eib
        Q2VC81_RHIOR | Q2VC812vq4 4bfn 4bfo

(-) Related Entries Specified in the PDB File

2v8m CARBOHYDRATE-BINDING OF THE STARCH BINDING DOMAIN OF RHIZOPUS ORYZAE GLUCOAMYLASE IN COMPLEX WITH BETA-CYCLODEXTRIN AND MALTOHEPTAOSE
2vq4 CARBOHYDRATE-BINDING OF THE STARCH BINDING DOMAIN OF RHIZOPUS ORYZAE GLUCOAMYLASE IN COMPLEX WITH BETA- CYCLODEXTRIN AND MALTOHEPTAOSE