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(-) Description

Title :  CYCLOMALTODEXTRINASE FROM FLAVOBACTERIUM SP. NO. 92: FROM DNA SEQUENCE TO PROTEIN STRUCTURE
 
Authors :  H. B. Fritzsche, T. Schwede, S. Jelakovic, G. E. Schulz
Date :  03 Sep 02  (Deposition) - 14 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cyclomaltodextrinase, Signal, Hydrolase, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. B. Fritzsche, T. Schwede, G. E. Schulz
Covalent And Three-Dimensional Structure Of The Cyclodextrinase From Flavobacterium Sp. No. 92.
Eur. J. Biochem. V. 270 2332 2003
PubMed-ID: 12752453  |  Reference-DOI: 10.1046/J.1432-1033.2003.03603.X

(-) 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: 469008
    Organism Common: FLAVOBACTERIUM
    Organism Scientific: FLAVOBACTERIUM SP.
    Organism Taxid: 239
    Strain: NO 92
    Synonym: CDASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 52)

Asymmetric Unit (2, 52)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MSE48Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:119 , ASP A:121 , ASN A:124 , ASP A:125 , GLY A:144 , ASP A:146 , HOH A:2093BINDING SITE FOR RESIDUE CA A 700
2AC2SOFTWARESER A:222 , THR A:270 , ASP A:280 , TYR A:315 , HOH A:2184 , HOH A:2209 , HOH A:2216BINDING SITE FOR RESIDUE CA A 701
3AC3SOFTWAREASN B:119 , ASP B:121 , ASN B:124 , ASP B:125 , GLY B:144 , ASP B:146 , HOH B:2125BINDING SITE FOR RESIDUE CA B 700
4AC4SOFTWARESER B:222 , THR B:270 , ASP B:280 , TYR B:315 , HOH B:2158 , HOH B:2163BINDING SITE FOR RESIDUE CA B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H3G)

(-) 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 1H3G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H3G)

(-) Exons   (0, 0)

(no "Exon" information available for 1H3G)

(-) 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:598
 aligned with Q8KKG0_9FLAO | Q8KKG0 from UniProtKB/TrEMBL  Length:619

    Alignment length:598
                                    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 PTAIEHMEPPFWWAGMQHKGLQLMVHGRDIGRMEAALDYPGVRLVSTTRVPNANYLFVDLEIGPEAQPGSFDIVFKGDGRSERYRYRLLAREQGSAQRQGFGPGDAIYQIMPDRFANGDPSNDNVAGMREQADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWPTPLVENDAAAYSYHGYAATDHYRIDPRYGSNEDFVRLSTEARKRGMGLIQDVVLSHIGKHHWWMKDLPTPDWINYGGKFVPTQHHRVAVQDPYAAQADSENFTKGWFVEGMPDLNQTNPLVANYLIQNNIWWIEYAGLSGLRIDTYGYSDGAFLTEYTRRLMAEYPRLNMVGEEWSTRVPVVARWQRGKANFDGYTSHLPSLMDFPLVDAMRNALSKTGEENGLNEVYETLSLDYLYPEPQNLVLFGGNHDMARMFSAAGEDFDRWRMNLVFLMTMPRIPQFYSGDEILMTSTVKGRDDASYRRDFPGGWAGDKANAFSGAGLTSQQRAAQDLVRKLANWRKNQPVIHNGRLMHFGPEENTWVYFRYNKDKRIMVAMNNNDKPMTLPTARFQEMLKGAPSGVDFLSGKTVGLGRELRLAPKSVVVIELPGLPE 618
               SCOP domains d1h3ga1 A:3-95 Cyclomaltodextrinase, N-terminal domain                                       d1h3ga3 A:96-517 Cyclomaltodextrinase, central domain                                                                                                                                                                                                                                                                                                                                                                                 d1h3ga2 A:518-600 Cyclomaltodextrinase                                              SCOP domains
               CATH domains 1h3gA01 A:3-92 Immunoglobulins                                                            ------1h3gA02 A:99-517 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                      1h3gA03 A:518-597 Golgi alpha-mannosidase II                                    --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...ee......eeeeeee.......eeee....eeeeeeee.....eeeeeeee......eeeeeeeee..eeeeeeeeee.................eeee.hhhh....hhh......................hhhhhh.hhhhhhh...eeee...ee..............eeeee......hhhhhhhhhhhhh...eeeeee.........hhhh..............................hhhhhhhhh.............hhhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhh....eeee......hhhhhh................ee..hhhhhhhhhhhh......hhhhhhhhhhhhhh...hhh.eee........hhhhh...hhhhhhhhhhhhh...eeeee..hhh..........hhhh.....................hhhhhhhhhhhhhhhhhhh..hhhhh.eeee......eeeeeee...eeeeeeee.....eeee....hhhh....eeee.....eee...eeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h3g A   3 PTAIEHmEPPFWWAGmQHKGLQLmVHGRDIGRmEAALDYPGVRLVSTTRVPNANYLFVDLEIGPEAQPGSFDIVFKGDGRSERYRYRLLAREQGSAQRQGFGPGDAIYQImPDRFANGDPSNDNVAGmREQADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWPTPLVENDAAAYSYHGYAATDHYRIDPRYGSNEDFVRLSTEARKRGmGLIQDVVLSHIGKHHWWmKDLPTPDWINYGGKFVPTQHHRVAVQDPYAAQADSENFTKGWFVEGmPDLNQTNPLVANYLIQNNIWWIEYAGLSGLRIDTYGYSDGAFLTEYTRRLmAEYPRLNmVGEEWSTRVPVVARWQRGKANFDGYTSHLPSLmDFPLVDAmRNALSKTGEENGLNEVYETLSLDYLYPEPQNLVLFGGNHDmARmFSAAGEDFDRWRmNLVFLmTmPRIPQFYSGDEILmTSTVKGRDDASYRRDFPGGWAGDKANAFSGAGLTSQQRAAQDLVRKLANWRKNQPVIHNGRLmHFGPEENTWVYFRYNKDKRImVAmNNNDKPmTLPTARFQEmLKGAPSGVDFLSGKTVGLGRELRLAPKSVVVIELPGLPE 600
                                  | 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        
                                  9-MSE   18-MSE  26-MSE   35-MSE                                                                       113-MSE          130-MSE                                                                            213-MSE           231-MSE                                        278-MSE                                            329-MSE 337-MSE                          370-MSE 378-MSE                                  419-MSE         435-MSE | |           457-MSE                                                        520-MSE              541-MSE     |       561-MSE                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                                             422-MSE            441-MSE                                                                                                544-MSE  |                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  443-MSE                                                                                                     551-MSE                                             


Chain B from PDB  Type:PROTEIN  Length:598
 aligned with Q8KKG0_9FLAO | Q8KKG0 from UniProtKB/TrEMBL  Length:619

    Alignment length:598
                                    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 PTAIEHMEPPFWWAGMQHKGLQLMVHGRDIGRMEAALDYPGVRLVSTTRVPNANYLFVDLEIGPEAQPGSFDIVFKGDGRSERYRYRLLAREQGSAQRQGFGPGDAIYQIMPDRFANGDPSNDNVAGMREQADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWPTPLVENDAAAYSYHGYAATDHYRIDPRYGSNEDFVRLSTEARKRGMGLIQDVVLSHIGKHHWWMKDLPTPDWINYGGKFVPTQHHRVAVQDPYAAQADSENFTKGWFVEGMPDLNQTNPLVANYLIQNNIWWIEYAGLSGLRIDTYGYSDGAFLTEYTRRLMAEYPRLNMVGEEWSTRVPVVARWQRGKANFDGYTSHLPSLMDFPLVDAMRNALSKTGEENGLNEVYETLSLDYLYPEPQNLVLFGGNHDMARMFSAAGEDFDRWRMNLVFLMTMPRIPQFYSGDEILMTSTVKGRDDASYRRDFPGGWAGDKANAFSGAGLTSQQRAAQDLVRKLANWRKNQPVIHNGRLMHFGPEENTWVYFRYNKDKRIMVAMNNNDKPMTLPTARFQEMLKGAPSGVDFLSGKTVGLGRELRLAPKSVVVIELPGLPE 618
               SCOP domains d1h3gb1 B:3-95 Cyclomaltodextrinase, N-terminal domain                                       d1h3gb3 B:96-517 Cyclomaltodextrinase, central domain                                                                                                                                                                                                                                                                                                                                                                                 d1h3gb2 B:518-600 Cyclomaltodextrinase                                              SCOP domains
               CATH domains 1h3gB01 B:3-92 Immunoglobulins                                                            ------1h3gB02 B:99-517 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                      1h3gB03 B:518-597 Golgi alpha-mannosidase II                                    --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...ee......eeeeeee.......eeee....eeeeeeee.....eeeeeeee......eeeeeeee....eeeeeeeee.................eeee.hhhh....hhh......................hhhhhh.hhhhhhh...eeee...ee..............eeeee......hhhhhhhhhhhhh...eeeeee.........hhhh..............................hhhhhhhhh.............hhhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhh....eeee......hhhhhh................ee..hhhhhhhhhhhh......hhhhhhhhhhhhhh...hhh.eee........hhhhh...hhhhhhhhhhhhh...eeeee..hhh..........hhhh.....................hhhhhhhhhhhhhhhhhhh..hhhhh.eeee......eeeeeeee..eeeeeeee.....eee.....hhhh....eeee.....eee....eee...eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h3g B   3 PTAIEHmEPPFWWAGmQHKGLQLmVHGRDIGRmEAALDYPGVRLVSTTRVPNANYLFVDLEIGPEAQPGSFDIVFKGDGRSERYRYRLLAREQGSAQRQGFGPGDAIYQImPDRFANGDPSNDNVAGmREQADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWPTPLVENDAAAYSYHGYAATDHYRIDPRYGSNEDFVRLSTEARKRGmGLIQDVVLSHIGKHHWWmKDLPTPDWINYGGKFVPTQHHRVAVQDPYAAQADSENFTKGWFVEGmPDLNQTNPLVANYLIQNNIWWIEYAGLSGLRIDTYGYSDGAFLTEYTRRLmAEYPRLNmVGEEWSTRVPVVARWQRGKANFDGYTSHLPSLmDFPLVDAmRNALSKTGEENGLNEVYETLSLDYLYPEPQNLVLFGGNHDmARmFSAAGEDFDRWRmNLVFLmTmPRIPQFYSGDEILmTSTVKGRDDASYRRDFPGGWAGDKANAFSGAGLTSQQRAAQDLVRKLANWRKNQPVIHNGRLmHFGPEENTWVYFRYNKDKRImVAmNNNDKPmTLPTARFQEmLKGAPSGVDFLSGKTVGLGRELRLAPKSVVVIELPGLPE 600
                                  | 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        
                                  9-MSE   18-MSE  26-MSE   35-MSE                                                                       113-MSE          130-MSE                                                                            213-MSE           231-MSE                                        278-MSE                                            329-MSE 337-MSE                          370-MSE 378-MSE                                  419-MSE         435-MSE | |           457-MSE                                                        520-MSE              541-MSE     |       561-MSE                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                                             422-MSE            441-MSE                                                                                                544-MSE  |                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  443-MSE                                                                                                     551-MSE
   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 1H3G)

(-) 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

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        Q8KKG0_9FLAO | Q8KKG0: 3edd 3ede 3edf 3edj 3edk

(-) Related Entries Specified in the PDB File

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