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(-) Description

Title :  STRUCTURAL BASE FOR CYCLODEXTRIN HYDROLYSIS
 
Authors :  S. Buedenbender, G. E. Schulz
Date :  03 Sep 08  (Deposition) - 03 Mar 09  (Release) - 03 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Alpha-Cyclodextrin Binding, Hydrolase, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Buedenbender, G. E. Schulz
Structural Base For Enzymatic Cyclodextrin Hydrolysis
J. Mol. Biol. V. 385 606 2009
PubMed-ID: 19014948  |  Reference-DOI: 10.1016/J.JMB.2008.10.085
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYCLOMALTODEXTRINASE
    Chains: A, B
    EC Number: 3.2.1.54
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CDASE
    Mutation: YES
    Organism Scientific: FLAVOBACTERIUM SP. 92
    Organism Taxid: 197856
    Synonym: FSPCMD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1ACX1Ligand/IonALPHA-CYCLODEXTRIN (CYCLOHEXA-AMYLOSE)
2CA4Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ACX-1Ligand/IonALPHA-CYCLODEXTRIN (CYCLOHEXA-AMYLOSE)
2CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACX2Ligand/IonALPHA-CYCLODEXTRIN (CYCLOHEXA-AMYLOSE)
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:119 , ASP A:121 , ASN A:124 , ASP A:125 , GLY A:144 , ASP A:146BINDING SITE FOR RESIDUE CA A 700
2AC2SOFTWARETHR A:270 , ASP A:280 , TYR A:315BINDING SITE FOR RESIDUE CA A 701
3AC3SOFTWAREASN B:119 , ASP B:121 , ASN B:124 , ASP B:125 , GLY B:144 , ASP B:146BINDING SITE FOR RESIDUE CA B 700
4AC4SOFTWARESER B:222 , THR B:270 , ASP B:280 , LEU B:281 , GLN B:283 , TYR B:315 , HOH B:845BINDING SITE FOR RESIDUE CA B 701
5AC5SOFTWARETYR B:178 , HIS B:181 , HIS B:251 , PHE B:274 , MET B:278 , ASP B:418 , ARG B:464 , ASP B:466 , ARG B:470 , HOH B:837BINDING SITE FOR RESIDUE ACX B 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EDD)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:10 -Pro A:11
2Glu B:10 -Pro B:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EDD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EDD)

(-) Exons   (0, 0)

(no "Exon" information available for 3EDD)

(-) 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:597
 aligned with Q8KKG0_9FLAO | Q8KKG0 from UniProtKB/TrEMBL  Length:619

    Alignment length:597
                                    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       540       550       560       570       580       590       600       610       
         Q8KKG0_9FLAO    21 PTAIEHMEPPFWWAGMQHKGLQLMVHGRDIGRMEAALDYPGVRLVSTTRVPNANYLFVDLEIGPEAQPGSFDIVFKGDGRSERYRYRLLAREQGSAQRQGFGPGDAIYQIMPDRFANGDPSNDNVAGMREQADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWPTPLVENDAAAYSYHGYAATDHYRIDPRYGSNEDFVRLSTEARKRGMGLIQDVVLSHIGKHHWWMKDLPTPDWINYGGKFVPTQHHRVAVQDPYAAQADSENFTKGWFVEGMPDLNQTNPLVANYLIQNNIWWIEYAGLSGLRIDTYGYSDGAFLTEYTRRLMAEYPRLNMVGEEWSTRVPVVARWQRGKANFDGYTSHLPSLMDFPLVDAMRNALSKTGEENGLNEVYETLSLDYLYPEPQNLVLFGGNHDMARMFSAAGEDFDRWRMNLVFLMTMPRIPQFYSGDEILMTSTVKGRDDASYRRDFPGGWAGDKANAFSGAGLTSQQRAAQDLVRKLANWRKNQPVIHNGRLMHFGPEENTWVYFRYNKDKRIMVAMNNNDKPMTLPTARFQEMLKGAPSGVDFLSGKTVGLGRELRLAPKSVVVIELPGLP 617
               SCOP domains d3edda1 A:3-95 automated matches                                                             d3edda2 A:96-517 automated matches                                                                                                                                                                                                                                                                                                                                                                                                    d3edda3 A:518-599 automated matches                                                SCOP domains
               CATH domains 3eddA01 A:3-92 Immunoglobulins                                                            ------3eddA02 A:99-517 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                      3eddA03 A:518-597 Golgi alpha-mannosidase II                                    -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...ee......eeeeeee..hhhhheeee....eeeeeeee.....eeeeeeee......eeeeeeeee..eeeeeeeeee.................eeeehhhhhh..hhhhh....................hhhhhhhhhhhhhhhh..eeee...ee..............eeeee.....hhhhhhhhhhhhhhh..eeeeee................................hhhhhhh...hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhh................ee.hhhhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhh.eee.......hhhhhh..hhhhhhhhhhhhhhh..eeeee.hhhhh........hhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhh.eeee......eeeeeee...eeeeeeee.....eeee...hhhhhh...eeee.....eee...eeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3edd A   3 PTAIEHMEPPFWWAGMQHKGLQLMVHGRDIGRMEAALDYPGVRLVSTTRVPNANYLFVDLEIGPEAQPGSFDIVFKGDGRSERYRYRLLAREQGSAQRQGFGPGDAIYQIMPDRFANGDPSNDNVAGMREQADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWPTPLVENDAAAYSYHGYAATDHYRIDPRYGSNEDFVRLSTEARKRGMGLIQDVVLSHIGKHHWWMKDLPTPDWINYGGKFVPTQHHRVAVQDPYAAQADSENFTKGWFVEGMPDLNQTNPLVANYLIQNNIWWIEYAGLSGLRIDTYGYSDGAFLTEYTRRLMAEYPRLNMVGQEWSTRVPVVARWQRGKANFDGYTSHLPSLMDFPLVDAMRNALSKTGEENGLNEVYETLSLDYLYPEPQNLVLFGGNHDMARMFSAAGEDFDRWRMNLVFLMTMPRIPQFYSGDEILMTSTVKGRDDASYRRDFPGGWAGDKANAFSGAGLTSQQRAAQDLVRKLANWRKNQPVIHNGRLMHFGPEENTWVYFRYNKDKRIMVAMNNNDKPMTLPTARFQEMLKGAPSGVDFLSGKTVGLGRELRLAPKSVVVIELPGLP 599
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       


Chain B from PDB  Type:PROTEIN  Length:597
 aligned with Q8KKG0_9FLAO | Q8KKG0 from UniProtKB/TrEMBL  Length:619

    Alignment length:597
                                    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       540       550       560       570       580       590       600       610       
         Q8KKG0_9FLAO    21 PTAIEHMEPPFWWAGMQHKGLQLMVHGRDIGRMEAALDYPGVRLVSTTRVPNANYLFVDLEIGPEAQPGSFDIVFKGDGRSERYRYRLLAREQGSAQRQGFGPGDAIYQIMPDRFANGDPSNDNVAGMREQADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWPTPLVENDAAAYSYHGYAATDHYRIDPRYGSNEDFVRLSTEARKRGMGLIQDVVLSHIGKHHWWMKDLPTPDWINYGGKFVPTQHHRVAVQDPYAAQADSENFTKGWFVEGMPDLNQTNPLVANYLIQNNIWWIEYAGLSGLRIDTYGYSDGAFLTEYTRRLMAEYPRLNMVGEEWSTRVPVVARWQRGKANFDGYTSHLPSLMDFPLVDAMRNALSKTGEENGLNEVYETLSLDYLYPEPQNLVLFGGNHDMARMFSAAGEDFDRWRMNLVFLMTMPRIPQFYSGDEILMTSTVKGRDDASYRRDFPGGWAGDKANAFSGAGLTSQQRAAQDLVRKLANWRKNQPVIHNGRLMHFGPEENTWVYFRYNKDKRIMVAMNNNDKPMTLPTARFQEMLKGAPSGVDFLSGKTVGLGRELRLAPKSVVVIELPGLP 617
               SCOP domains d3eddb1 B:3-95 automated matches                                                             d3eddb2 B:96-517 automated matches                                                                                                                                                                                                                                                                                                                                                                                                    d3eddb3 B:518-599 automated matches                                                SCOP domains
               CATH domains 3eddB01 B:3-92 Immunoglobulins                                                            ------3eddB02 B:99-517 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                      3eddB03 B:518-597 Golgi alpha-mannosidase II                                    -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee......eeeeeee..hhhhheeee....eeeeeeee.....eeeeeeee......eeeeeeeee..eee..eeeee.................eeeehhhhhh..hhhhh....................hhhhhhhhhhhhhhhh..eeee...ee..............eeeee.....hhhhhhhhhhhhhh...ee.eee................................hhhhhhh...hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhh....eee.....hhhhhhh................ee.hhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhh.eee.......hhhhhh..hhhhhhhhhhhhhhh..eeeee.hhhhh........hhhhhh....................hhhhhhhhhhhhhhhhhhh.hhhhhh.eeee......eeeeeee...eeeeeeee.....eeee...hhhhhh...eeee.....eee...eeee...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3edd B   3 PTAIEHMEPPFWWAGMQHKGLQLMVHGRDIGRMEAALDYPGVRLVSTTRVPNANYLFVDLEIGPEAQPGSFDIVFKGDGRSERYRYRLLAREQGSAQRQGFGPGDAIYQIMPDRFANGDPSNDNVAGMREQADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWPTPLVENDAAAYSYHGYAATDHYRIDPRYGSNEDFVRLSTEARKRGMGLIQDVVLSHIGKHHWWMKDLPTPDWINYGGKFVPTQHHRVAVQDPYAAQADSENFTKGWFVEGMPDLNQTNPLVANYLIQNNIWWIEYAGLSGLRIDTYGYSDGAFLTEYTRRLMAEYPRLNMVGQEWSTRVPVVARWQRGKANFDGYTSHLPSLMDFPLVDAMRNALSKTGEENGLNEVYETLSLDYLYPEPQNLVLFGGNHDMARMFSAAGEDFDRWRMNLVFLMTMPRIPQFYSGDEILMTSTVKGRDDASYRRDFPGGWAGDKANAFSGAGLTSQQRAAQDLVRKLANWRKNQPVIHNGRLMHFGPEENTWVYFRYNKDKRIMVAMNNNDKPMTLPTARFQEMLKGAPSGVDFLSGKTVGLGRELRLAPKSVVVIELPGLP 599
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592
   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  (3, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EDD)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8KKG0_9FLAO | Q8KKG0)
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:0047798    cyclomaltodextrinase activity    Catalysis of the reaction: H2O + cyclomaltodextrin = linear maltodextrin.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8KKG0_9FLAO | Q8KKG0: 1h3g 3ede 3edf 3edj 3edk

(-) Related Entries Specified in the PDB File

3ede CONTACT MUTANT
3edf ALPHA-CYCLODEXTRIN COMPLEX
3edj BETA-CYCLODEXTRIN COMPLEX
3edk GAMMA-CYCLODEXTRIN COMPLEX