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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STARCH-BINDING DOMAIN FROM RHIZOPUS ORYZAE GLUCOAMYLASE IN COMPLEX WITH ISOMALTOTETRAOSE
 
Authors :  C. H. Chu, K. M. Li, S. W. Lin, Y. J. Sun
Date :  21 Mar 13  (Deposition) - 23 Oct 13  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.32
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Carbohydrate Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chu, K. Li, S. Lin, M. D. Chang, T. Jiang, Y. Sun
Crystal Structures Of Starch Binding Domain From Rhizopus Oryzae Glucoamylase In Complex With Isomaltooligosaccharide: Insights Into Polysaccharide Binding Mechanism Of Cbm21 Family.
Proteins V. 82 1079 2014
PubMed-ID: 24108499  |  Reference-DOI: 10.1002/PROT.24446

(-) Compounds

Molecule 1 - GLUCOAMYLASE
    Chains: A
    EC Number: 3.2.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET23A
    Expression System Vector Type: PLASMID
    Fragment: STARCH BINDING DOMAIN, RESIDUES 26-131
    Organism Scientific: RHIZOPUS ORYZAE
    Organism Taxid: 64495

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1GLC4Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:1 , ASN A:29 , TYR A:32 , LYS A:34 , TRP A:47 , PHE A:58 , GLU A:68 , TRP A:70 , TYR A:83 , TYR A:94 , ASN A:96 , ASN A:101 , HOH A:2054 , HOH A:2067 , HOH A:2128 , HOH A:2137 , HOH A:2138 , HOH A:2139 , HOH A:2140BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1106 TO 1109

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BFN)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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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.....eeeeeeee.....hhhhh.eee.eeeee.....eeeeeeeee.....eeeeeeee..eeeee......ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4bfn A   1 ASIPSSASVQLDSYNYDGSTFSGKIYVKNIAYSKKVTVVYADGSDNWNNNGNIIAASFSGPISGSNYEYWTFSASVKGIKEFYIKYEVSGKTYYDNNNSANYQVST 106
                                    10        20        30        40        50        60        70        80        90       100
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4BFN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

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.

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  4bfn
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  Q2VC81_RHIOR | Q2VC81
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q2VC81_RHIOR | Q2VC81: 2v8l 2v8m
UniProtKB/TrEMBL
        Q2VC81_RHIOR | Q2VC81: 2vq4 4bfo

(-) Related Entries Specified in the PDB File

4bfo CRYSTAL STRUCTURE OF THE STARCH-BINDING DOMAIN FROM RHIZOPUS ORYZAE GLUCOAMYLASE IN COMPLEX WITH ISOMALTOTRIOSE