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(-) Description

Title :  COMPLEX OF ALPHA-AMYLASE II (TVA II) FROM THERMOACTINOMYCES VULGARIS R-47 WITH BETA-CYCLODEXTRIN BASED ON A CO-CRYSTALLIZATION WITH METHYL BETA-CYCLODEXTRIN
 
Authors :  T. Yokota, T. Tonozuka, Y. Shimura, K. Ichikawa, S. Kamitori, Y. Sakano
Date :  16 Jul 01  (Deposition) - 01 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pullulan, Cyclodextrin, Neopullulanase, Methyl Beta- Cyclodextrin, Beta-Cyclodextrin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yokota, T. Tonozuka, Y. Shimura, K. Ichikawa, S. Kamitori, Y. Sakano
Structures Of Thermoactinomyces Vulgaris R-47 Alpha-Amylase Ii Complexed With Substrate Analogues.
Biosci. Biotechnol. Biochem. V. 65 619 2001
PubMed-ID: 11330677  |  Reference-DOI: 10.1271/BBB.65.619
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE II
    Chains: A, B
    EC Number: 3.2.1.135
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTND325N
    Expression System Strain: MV1184
    Expression System Taxid: 562
    Expression System Vector: PUC119
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMOACTINOMYCES VULGARIS
    Organism Taxid: 2026
    Strain: R-47
    Synonym: NEOPULLULANASE

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1BCD2Ligand/IonBETA-CYCLODEXTRIN
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BCD1Ligand/IonBETA-CYCLODEXTRIN
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BCD1Ligand/IonBETA-CYCLODEXTRIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:204 , PHE A:286 , MET A:293 , ASN A:325 , GLU A:354 , TRP A:356 , HIS A:420 , ASP A:421 , ARG A:469 , ARG B:44 , ALA B:46BINDING SITE FOR RESIDUE BCD A 601
2AC2SOFTWARETYR A:45 , HIS B:164 , HIS B:202 , TYR B:204 , PHE B:286 , MET B:293 , ASN B:325 , GLU B:354 , TRP B:356 , ASP B:421BINDING SITE FOR RESIDUE BCD B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JL8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:273 -Pro A:274
2Asp A:465 -Pro A:466
3Phe B:273 -Pro B:274
4Asp B:465 -Pro B:466

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JL8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JL8)

(-) Exons   (0, 0)

(no "Exon" information available for 1JL8)

(-) 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:585
 aligned with NEPU2_THEVU | Q08751 from UniProtKB/Swiss-Prot  Length:585

    Alignment length:585
                                    10        20        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     
          NEPU2_THEVU     1 MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEEELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDPPGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPSHHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFFAFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTENPEVKEYLFDVARFWMEQGIDGWRLDVANEVDHAFWREFRRLVKSLNPDALIVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTRARMLYPEQAAQGLWNLLDSHDTERFLTSCGGNEAKFRLAVLFQMTYLGTPLIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASLTRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR 585
               SCOP domains d1jl8a1 A:1-120 Maltogenic amylase, N-terminal domain N                                                                 d1jl8a3 A:121-502 Maltogenic amylase, central domain                                                                                                                                                                                                                                                                                                                                          d1jl8a2 A:503-585 Maltogenic amylase                                                SCOP domains
               CATH domains 1jl8A01 A:1-121 Immunoglobulins                                                                                          1jl8A02 A:122-242,A:298-502 Glycosidases                                                                                 -------------------------------------------------------1jl8A02 A:122-242,A:298-502 Glycosidases                                                                                                                                                                     1jl8A04 A:503-585 Golgi alpha-mannosidase II                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh........eee....eeeeeeeee.....eeeeeee..........eeee.eeeee...eeeeeeeee.....eeeeeeee.....eeee....ee........eee...hhhhh...hhhhhh..eeeehhhhhh............................hhhhhhhhhhhhhhhh..eeee...ee..........eeeee.....hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhh.hhhh................................hhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhh......ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhh..eee.......hhhhhh..hhhhhhhhhhhhh....eeeee.hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee....eeeeeeee..eeeeeeee.....eeeeee.........ee............eeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jl8 A   1 MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEEELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDPPGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPSHHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFFAFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTENPEVKEYLFDVARFWMEQGIDGWRLNVANEVDHAFWREFRRLVKSLNPDALIVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTRARMLYPEQAAQGLWNLLDSHDTERFLTSCGGNEAKFRLAVLFQMTYLGTPLIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASLTRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR 585
                                    10        20        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     


Chain B from PDB  Type:PROTEIN  Length:585
 aligned with NEPU2_THEVU | Q08751 from UniProtKB/Swiss-Prot  Length:585

    Alignment length:585
                                    10        20        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     
          NEPU2_THEVU     1 MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEEELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDPPGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPSHHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFFAFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTENPEVKEYLFDVARFWMEQGIDGWRLDVANEVDHAFWREFRRLVKSLNPDALIVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTRARMLYPEQAAQGLWNLLDSHDTERFLTSCGGNEAKFRLAVLFQMTYLGTPLIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASLTRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR 585
               SCOP domains d1jl8b1 B:1-120 Maltogenic amylase, N-terminal domain N                                                                 d1jl8b3 B:121-502 Maltogenic amylase, central domain                                                                                                                                                                                                                                                                                                                                          d1jl8b2 B:503-585 Maltogenic amylase                                                SCOP domains
               CATH domains 1jl8B01 B:1-121 Immunoglobulins                                                                                          1jl8B02 B:122-242,B:298-502 Glycosidases                                                                                 -------------------------------------------------------1jl8B02 B:122-242,B:298-502 Glycosidases                                                                                                                                                                     1jl8B04 B:503-585 Golgi alpha-mannosidase II                                        CATH domains
           Pfam domains (1) Alpha-amylase_N-1jl8B05 B:1-117                                                                                      ----------------------------------------------------Alpha-amylase-1jl8B03 B:170-466                                                                                                                                                                                                                                                                          -----------------------------------------Alpha-amylase_C-1jl8B01 B:508-583                                           -- Pfam domains (1)
           Pfam domains (2) Alpha-amylase_N-1jl8B06 B:1-117                                                                                      ----------------------------------------------------Alpha-amylase-1jl8B04 B:170-466                                                                                                                                                                                                                                                                          -----------------------------------------Alpha-amylase_C-1jl8B02 B:508-583                                           -- Pfam domains (2)
         Sec.struct. author .hhhhh........eeeee..eeeeeeeee.....eeeeeee..........eeee.eeeee...eeeeeeeee.....eeeeeeee.....eeee....ee.hhhhhh.eee...hhhhh...hhhhhh..eeeehhhhhh..hhhhh.....................hhhhhhhhhhhhhhhh..eeee...ee..........eeeee.....hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhh.hhhh................................hhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhh......ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhh..eee.......hhhhhh..hhhhhhhhhhhhhhh..eeeee.hhhhh......hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeeeeee..eeeeeeee.....eeeeee........eee....ee......eeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jl8 B   1 MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEEELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDPPGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPSHHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFFAFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTENPEVKEYLFDVARFWMEQGIDGWRLNVANEVDHAFWREFRRLVKSLNPDALIVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTRARMLYPEQAAQGLWNLLDSHDTERFLTSCGGNEAKFRLAVLFQMTYLGTPLIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASLTRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR 585
                                    10        20        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
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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  (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  (3, 6)

Asymmetric Unit
(-)
Clan: GHD (106)
(-)
Clan: Glyco_hydro_tim (488)
(-)
Clan: no clan defined [family: Alpha-amylase_N] (16)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NEPU2_THEVU | Q08751)
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: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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0031216    neopullulanase activity    Catalysis of the hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose).
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/Swiss-Prot
        NEPU2_THEVU | Q08751: 1bvz 1g1y 1jf5 1jf6 1ji2 1jib 1vb9 1vfm 1vfo 1vfu 1wzk 1wzl 1wzm 2d2o 3a6o

(-) Related Entries Specified in the PDB File

1bvz 1BVZ CONTAINS THE SAME PROTEIN(WILD TYPE)
1g1y 1G1Y CONTAINS THE SAME PROTEIN(MUTANT E354A) COMPLEXED WITH BETA-CYCLODEXTRIN
1jib 1JIB CONTAINS THE SAME PROTEIN(MUTANT D325N) COMPLEXED WITH MALTOTETRAOSE BASED ON A CRYSTAL SOAKED WITH MALTOHEXAOSE