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(-) Description

Title :  GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN COMPLEX WITH CYCLODEXTRIN, NMR, MINIMIZED AVERAGE STRUCTURE
 
Authors :  K. Sorimachi, M. -F. Le Gal-Coeffet, G. Williamson, D. B. Archer, M. P. Williamson
Date :  10 Feb 97  (Deposition) - 07 Jul 97  (Release) - 19 May 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Hydrolase, Starch Binding Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Sorimachi, M. F. Le Gal-Coeffet, G. Williamson, D. B. Archer, M. P. Williamson
Solution Structure Of The Granular Starch Binding Domain Of Aspergillus Niger Glucoamylase Bound To Beta-Cyclodextrin.
Structure V. 5 647 1997
PubMed-ID: 9195884  |  Reference-DOI: 10.1016/S0969-2126(97)00220-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOAMYLASE
    ChainsA
    EC Number3.2.1.3
    EngineeredYES
    Expression SystemASPERGILLUS NIGER
    Expression System GeneA. NIGER GLAA
    Expression System PlasmidPIGF
    Expression System Taxid5061
    FragmentBINDING DOMAIN, RESIDUES 509 - 616
    Organism ScientificASPERGILLUS NIGER
    Organism Taxid5061
    StrainAB4.1
    Synonym1,4-ALPHA-D-GLUCAN GLUCOHYDROLASE

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

NMR Structure (3, 14)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2GLC11Ligand/IonALPHA-D-GLUCOSE
3GLO1Ligand/IonD-GLUCOSE IN LINEAR FORM

(-) Sites  (14, 14)

NMR Structure (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREBGC A:2 , GLC A:7 , TRP A:590BINDING SITE FOR RESIDUE GLC A 1
02AC2SOFTWAREGLC A:1 , GLC A:3 , TRP A:543 , GLU A:544 , THR A:545 , TRP A:590BINDING SITE FOR RESIDUE BGC A 2
03AC3SOFTWAREBGC A:2 , GLC A:4 , TRP A:543 , GLU A:544BINDING SITE FOR RESIDUE GLC A 3
04AC4SOFTWAREGLC A:3 , BGC A:5BINDING SITE FOR RESIDUE GLC A 4
05AC5SOFTWAREGLC A:4 , GLO A:6 , SER A:536 , TRP A:543BINDING SITE FOR RESIDUE BGC A 5
06AC6SOFTWAREBGC A:5 , GLC A:7 , TRP A:543BINDING SITE FOR RESIDUE GLO A 6
07AC7SOFTWAREGLC A:1 , GLO A:6BINDING SITE FOR RESIDUE GLC A 7
08AC8SOFTWARETYR A:556 , THR A:557 , SER A:558 , PRO A:561 , LEU A:562 , GLC A:618B , GLC A:623BBINDING SITE FOR RESIDUE GLC A 617B
09AC9SOFTWAREGLC A:617B , GLC A:619B , GLC A:620B , GLC A:623BBINDING SITE FOR RESIDUE GLC A 618B
10BC1SOFTWAREGLC A:618B , GLC A:620B , GLC A:621B , GLC A:622BBINDING SITE FOR RESIDUE GLC A 619B
11BC2SOFTWARETYR A:527 , SER A:558 , GLC A:618B , GLC A:619B , GLC A:621BBINDING SITE FOR RESIDUE GLC A 620B
12BC3SOFTWAREGLC A:619B , GLC A:620B , GLC A:622BBINDING SITE FOR RESIDUE GLC A 621B
13BC4SOFTWAREGLC A:619B , GLC A:621B , GLC A:623BBINDING SITE FOR RESIDUE GLC A 622B
14BC5SOFTWAREALA A:523 , TYR A:556 , PRO A:561 , LEU A:562 , GLC A:617B , GLC A:618B , GLC A:622BBINDING SITE FOR RESIDUE GLC A 623B

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:509 -A:604

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1AC0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AC0)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBM20PS51166 CBM20 (carbohydrate binding type-20) domain profile.AMYG_ASPAW533-640  1A:509-616
AMYG_ASPNG533-640  1A:509-616

(-) Exons   (0, 0)

(no "Exon" information available for 1AC0)

(-) Sequences/Alignments

NMR Structure
   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:108
 aligned with AMYG_ASPAW | P69327 from UniProtKB/Swiss-Prot  Length:640

    Alignment length:108
                                   542       552       562       572       582       592       602       612       622       632        
           AMYG_ASPAW   533 CTTPTAVAVTFDLTATTTYGENIYLVGSISQLGDWETSDGIALSADKYTSSDPLWYVTVTLPAGESFEYKFIRIESDDSVEWESDPNREYTVPQACGTSTATVTDTWR 640
               SCOP domains d1ac0a_ A: Glucoamylase, granular starch-binding domain                                                      SCOP domains
               CATH domains 1ac0A00 A:509-616 Immunoglobulins                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeee......eeeeeee........hhh.eeee........eeeeeeeeeee.eeeeeeeeee......eee...............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) CBM20  PDB: A:509-616 UniProt: 533-640                                                                       PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1ac0 A 509 CTTPTAVAVTFDLTATTTYGENIYLVGSISQLGDWETSDGIALSADKYTSSDPLWYVTVTLPAGESFEYKFIRIESDDSVEWESDPNREYTVPQACGTSTATVTDTWR 616
                                   518       528       538       548       558       568       578       588       598       608        

Chain A from PDB  Type:PROTEIN  Length:108
 aligned with AMYG_ASPNG | P69328 from UniProtKB/Swiss-Prot  Length:640

    Alignment length:108
                                   542       552       562       572       582       592       602       612       622       632        
           AMYG_ASPNG   533 CTTPTAVAVTFDLTATTTYGENIYLVGSISQLGDWETSDGIALSADKYTSSDPLWYVTVTLPAGESFEYKFIRIESDDSVEWESDPNREYTVPQACGTSTATVTDTWR 640
               SCOP domains d1ac0a_ A: Glucoamylase, granular starch-binding domain                                                      SCOP domains
               CATH domains 1ac0A00 A:509-616 Immunoglobulins                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeee......eeeeeee........hhh.eeee........eeeeeeeeeee.eeeeeeeeee......eee...............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE CBM20  PDB: A:509-616 UniProt: 533-640                                                                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1ac0 A 509 CTTPTAVAVTFDLTATTTYGENIYLVGSISQLGDWETSDGIALSADKYTSSDPLWYVTVTLPAGESFEYKFIRIESDDSVEWESDPNREYTVPQACGTSTATVTDTWR 616
                                   518       528       538       548       558       568       578       588       598       608        

   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  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AC0)

(-) Gene Ontology  (11, 21)

NMR Structure(hide GO term definitions)
Chain A   (AMYG_ASPAW | P69327)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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: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:2001070    starch binding    Interacting selectively and non-covalently with starch.
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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    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   (AMYG_ASPNG | P69328)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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: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:2001070    starch binding    Interacting selectively and non-covalently with starch.
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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    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.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMYG_ASPAW | P693271acz 1agm 1dog 1gah 1gai 1glm 3gly
        AMYG_ASPNG | P693281acz 1kul 1kum 3eqa

(-) Related Entries Specified in the PDB File

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