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(-) Description

Title :  CRYSTAL STRUCTURE OF NOSTOC PUNCTIFORME DEBRANCHING ENZYME( NPDE)(ACARBOSE SOAKED)
 
Authors :  A. -B. Dumbrepatil, H. -N. Song, J. -H. Choi, K. -H. Park, E. -J. Woo
Date :  10 Mar 09  (Deposition) - 29 Sep 09  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cd/Pul-Hydrolyzing Enzymes, Hydrolase, Glycosidase, Neopullulanse (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. -B. Dumbrepatil, J. -H. Choi, J. T. Park, M. J. Kim, T. J. Kim, E. -J. Woo, K. -H. Park
Structural Features Of The Nostoc Punctiforme Debranching Enzyme Reveal The Basis Of Its Mechanism And Substrate Specificity.
Proteins V. 78 348 2010
PubMed-ID: 19768689  |  Reference-DOI: 10.1002/PROT.22548

(-) Compounds

Molecule 1 - ALPHA AMYLASE, CATALYTIC REGION
    Chains: A
    EC Number: 3.2.1.54
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: NOSTOC PUNCTIFORME
    Organism Taxid: 272131
    Synonym: NOSTOC PUNCTIFORME DEBRANCHING ENZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2WC7)

(-) Sites  (0, 0)

(no "Site" information available for 2WC7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WC7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Trp A:156 -Pro A:157
2Tyr A:288 -Pro A:289

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WC7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WC7)

(-) Exons   (0, 0)

(no "Exon" information available for 2WC7)

(-) 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:470
 aligned with B2IUW9_NOSP7 | B2IUW9 from UniProtKB/TrEMBL  Length:488

    Alignment length:485
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481     
         B2IUW9_NOSP7     2 QIQTPDWVKHAVFYQIFPDRFARSKQPRKRLLQEARWEDWDSMPTLQGYKGGDLWGIMEDLDYIQNLGINAIYFTPIFQSASNHRYHTHDYYQVDPMLGGNEAFKELLDAAHQRNIKVVLDGVFNHSSRGFFFFHDVLENGPHSPWVNWFKIEGWPLSPYNGEFPANYVGWAGNRALPEFNHDNPEVREYIMEIAEYWLKFGIDGWRLDVPFEIKTPGFWQEFRDRTKAINPEAYIVGEVWGDSRQWLDGTQFDGVMNYLFAGPTIAFAAGDRVVLEQVQSRDYQPYPPLFAAEYATKIQEVLQLYPWEIQLTQLNLLASHDTARLMTIAGGDIASVELSTLLLLTFPGAPSIYYGDEVGLPGGIDPDSRRGFPLEANWNQEIFNTHRQLITIRQTYPALRTGDYQVLYAQGQLYLFARTLGTEELIIAINAGTSSATANVDVASLHTQPNKLLYGTAEAEWNGEEGTQQLSLTLPARSGCILGT 486
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------Alpha-amylase-2wc7A02 A:53-367                                                                                                                                                                                                                                                                                                 ------ --------DUF3459-2wc7A01 A:387-484                                                                         -- Pfam domains
         Sec.struct. author ....hhhhhh..eeeehhhhh..............hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeee...eee.......eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhh.hhhh.....................hhhh.........hhhhhhhhhhhhhhhhhhh..eeee.hhhhh...hhhhhhhhhhhhhh...eeee.....hhhhh......ee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhhh..ee........hhhhhh..hhhhhhhhhhhhhh...eeeee.hhhhh......----......-..hhhhhhhhhhhhhhhhhhhhhhhheeeeeeee..eeeeeeee..eeeeeeee.....eeeeee..........eee...----------.eeeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wc7 A   2 QIQTPDWVKHAVFYQIFPDRFARSKQPRKRLLQEARWEDWDSMPTLQGYKGGDLWGIMEDLDYIQNLGINAIYFTPIFQSASNHRYHTHDYYQVDPMLGGNEAFKELLDAAHQRNIKVVLDGVFNHSSRGFFFFHDVLENGPHSPWVNWFKIEGWPLSPYNGEFPANYVGWAGNRALPEFNHDNPEVREYIMEIAEYWLKFGIDGWRLDVPFEIKTPGFWQEFRDRTKAINPEAYIVGEVWGDSRQWLDGTQFDGVMNYLFAGPTIAFAAGDRVVLEQVQSRDYQPYPPLFAAEYATKIQEVLQLYPWEIQLTQLNLLASHDTARLMTIAGGDIASVELSTLLLLTFPGAPSIYYGDEVGLPGGID----RGFPLE-NWNQEIFNTHRQLITIRQTYPALRTGDYQVLYAQGQLYLFARTLGTEELIIAINAGTSSATANVDVASLHTQPNKLLYGTA----------QQLSLTLPARSGCILGT 486
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361     |   -|    | 381       391       401       411       421       431       441       451       | -       471       481     
                                                                                                                                                                                                                                                                                                                                                                                                       367  372  377 |                                                                             459        470                
                                                                                                                                                                                                                                                                                                                                                                                                                   379
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 2WC7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WC7)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: GHD (106)
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (B2IUW9_NOSP7 | B2IUW9)
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.
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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    Trp A:156 - Pro A:157   [ RasMol ]  
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  3.2.1.54
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 Related Entries

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

UniProtKB/TrEMBL
        B2IUW9_NOSP7 | B2IUW9: 2wcs 2wkg

(-) Related Entries Specified in the PDB File

2wcs CRYSTAL STRUCTURE OF DEBRANCHING ENZYME FROM NOSTOC PUNCTIFORME (NPDE)
2wkg NOSTOC PUNCTIFORME DEBRANCHING ENZYME (NPDE) (NATIVE FORM)