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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 :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
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
    Chains: A, B, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 34)

Asymmetric Unit (2, 34)
No.NameCountTypeFull Name
1GLC28Ligand/IonALPHA-D-GLUCOSE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GLC7Ligand/IonALPHA-D-GLUCOSE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1GLC7Ligand/IonALPHA-D-GLUCOSE
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1GLC7Ligand/IonALPHA-D-GLUCOSE
2SO41Ligand/IonSULFATE ION
Biological Unit 4 (2, 9)
No.NameCountTypeFull Name
1GLC7Ligand/IonALPHA-D-GLUCOSE
2SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:7 , SER A:8 , TYR A:93 , HOH A:2086 , HOH A:2087BINDING SITE FOR RESIDUE SO4 A1117
02AC2SOFTWAREASN A:98 , ASN B:96 , ASN B:98 , HOH B:2065 , HOH B:2083 , HOH B:2084BINDING SITE FOR RESIDUE SO4 B1117
03AC3SOFTWARESER B:8 , TYR B:93 , HOH B:2086 , HOH B:2088 , HOH B:2089BINDING SITE FOR RESIDUE SO4 B1118
04AC4SOFTWAREALA C:7 , SER C:8 , TYR C:93 , HOH C:2059 , HOH C:2060 , HOH C:2061BINDING SITE FOR RESIDUE SO4 C1110
05AC5SOFTWARESER D:8 , TYR D:93 , HOH D:2077 , HOH D:2078BINDING SITE FOR RESIDUE SO4 D1111
06AC6SOFTWAREPRO D:4 , SER D:5 , SER D:6 , ALA D:7BINDING SITE FOR RESIDUE SO4 D1112
07AC7SOFTWAREASN A:29 , TYR A:32 , SER A:33 , LYS A:34 , PHE A:58 , GLU A:68 , TRP A:70 , HOH A:2041 , HOH A:2077 , HOH A:2078 , HOH A:2079BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1001 TO 1007
08AC8SOFTWAREASN B:29 , TYR B:32 , SER B:33 , LYS B:34 , PHE B:58 , GLU B:68 , HOH B:2016 , HOH B:2018 , HOH B:2072 , HOH B:2073 , HOH B:2074 , HOH B:2075BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 1001 TO 1007
09AC9SOFTWAREASP A:17 , TRP A:47 , ASN A:50 , LYS A:77 , TYR A:94 , ASN A:96 , ASN A:101 , HOH A:2011 , ASP B:17 , GLY B:18 , THR B:106 , ASN C:29 , TYR C:32 , SER C:33 , LYS C:34 , PHE C:58 , GLU C:68 , TRP C:70 , HOH C:2058BINDING SITE FOR CHAIN C OF POLYSACCHARIDE RESIDUES 1001 TO 1007
10BC1SOFTWARESER A:2 , TRP B:47 , ASN B:50 , TYR B:83 , TYR B:94 , ASN B:96 , ASN B:101 , ASN D:29 , TYR D:32 , SER D:33 , LYS D:34 , PHE D:58 , GLU D:68 , HOH D:2071 , HOH D:2072 , HOH D:2073 , HOH D:2074 , HOH D:2075 , HOH D:2076BINDING SITE FOR CHAIN D OF POLYSACCHARIDE RESIDUES 1001 TO 1007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V8M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V8M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V8M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V8M)

(-) Exons   (0, 0)

(no "Exon" information available for 2V8M)

(-) Sequences/Alignments

Asymmetric 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......eeeeee............eee.eeeee.....eeeeeeeee.....eeeeeeee..eeeee......ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2v8m 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......eeeeee............eee.eeeee.....eeeeeeeee.....eeeeeeee..eeeee......ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2v8m A   1 ASIPSSASVQLDSYNYDGSTFSGKIYVKNIAYSKKVTVVYADGSDNWNNNGNIIAASFSGPISGSNYEYWTFSASVKGIKEFYIKYEVSGKTYYDNNNSANYQVST 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain B 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.....eeeeeeeee..........eee.eeeee.....eeeeeeeee...eeeeeeeeee..eeeee......ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2v8m B   1 ASIPSSASVQLDSYNYDGSTFSGKIYVKNIAYSKKVTVVYADGSDNWNNNGNIIAASFSGPISGSNYEYWTFSASVKGIKEFYIKYEVSGKTYYDNNNSANYQVST 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain B 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.....eeeeeeeee..........eee.eeeee.....eeeeeeeee...eeeeeeeeee..eeeee......ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2v8m B   1 ASIPSSASVQLDSYNYDGSTFSGKIYVKNIAYSKKVTVVYADGSDNWNNNGNIIAASFSGPISGSNYEYWTFSASVKGIKEFYIKYEVSGKTYYDNNNSANYQVST 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain C 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....eeeeeeee.....eeeeeeee...........eee.eeee......eeeeeeee......eeeeeeee..eeeee......ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2v8m C   1 ASIPSSASVQLDSYNYDGSTFSGKIYVKNIAYSKKVTVVYADGSDNWNNNGNIIAASFSGPISGSNYEYWTFSASVKGIKEFYIKYEVSGKTYYDNNNSANYQVST 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain C 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....eeeeeeee.....eeeeeeee...........eee.eeee......eeeeeeee......eeeeeeee..eeeee......ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2v8m C   1 ASIPSSASVQLDSYNYDGSTFSGKIYVKNIAYSKKVTVVYADGSDNWNNNGNIIAASFSGPISGSNYEYWTFSASVKGIKEFYIKYEVSGKTYYDNNNSANYQVST 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain D 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
                 2v8m D   1 ASIPSSASVQLDSYNYDGSTFSGKIYVKNIAYSKKVTVVYADGSDNWNNNGNIIAASFSGPISGSNYEYWTFSASVKGIKEFYIKYEVSGKTYYDNNNSANYQVST 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain D 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
                 2v8m D   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 2V8M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V8M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V8M)

(-) Gene Ontology  (4, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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,B,C,D   (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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  2v8m
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  B7XC04_RHIOR | B7XC04
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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
UniProtKB/TrEMBL
        B7XC04_RHIOR | B7XC04: 2v8l 4eib
        Q2VC81_RHIOR | Q2VC81: 2vq4 4bfn 4bfo

(-) Related Entries Specified in the PDB File

2v8l 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