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(-) Description

Title :  CRYSTAL STRUCTURE OF MALTOHEXAOSE-PRODUCING AMYLASE COMPLEXED WITH PSEUDO-MALTONONAOSE
 
Authors :  R. Kanai, K. Haga, T. Akiba, K. Yamane, K. Harata
Date :  01 Sep 04  (Deposition) - 30 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Maltohexaose-Producing Amylase, Alpha-Amylase, Acarbose, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kanai, K. Haga, T. Akiba, K. Yamane, K. Harata
Biochemical And Crystallographic Analyses Of Maltohexaose-Producing Amylase From Alkalophilic Bacillus Sp. 707
Biochemistry V. 43 14047 2004
PubMed-ID: 15518553  |  Reference-DOI: 10.1021/BI048489M
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCAN 1,4-ALPHA-MALTOHEXAOSIDASE
    Chains: A
    EC Number: 3.2.1.98
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PTUB812
    Expression System Strain: 207-25
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 1416
    Strain: 707
    Synonym: G6-AMYLASE, MALTOHEXAOSE-PRODUCING AMYLASE, EXO- MALTOHEXAOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 17)

Asymmetric/Biological Unit (6, 17)
No.NameCountTypeFull Name
1ACI2Ligand/Ion6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
2CA3Ligand/IonCALCIUM ION
3GAL1Ligand/IonBETA-D-GALACTOSE
4GLC8Ligand/IonALPHA-D-GLUCOSE
5GLD2Ligand/Ion4,6-DIDEOXYGLUCOSE
6NA1Ligand/IonSODIUM ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:72 , GLY A:110 , ALA A:111 , TRP A:140 , GLD A:602 , HOH A:733BINDING SITE FOR RESIDUE ACI A 601
02AC2SOFTWAREGLY A:110 , ALA A:111 , TRP A:140 , TYR A:203 , ACI A:601 , GLC A:603 , HOH A:734 , HOH A:735BINDING SITE FOR RESIDUE GLD A 602
03AC3SOFTWAREASP A:166 , MET A:202 , TYR A:203 , GLD A:602 , GLC A:604 , HOH A:734BINDING SITE FOR RESIDUE GLC A 603
04AC4SOFTWAREMET A:202 , TYR A:203 , GLC A:603 , GLC A:605 , HOH A:858 , HOH A:862BINDING SITE FOR RESIDUE GLC A 604
05AC5SOFTWARETRP A:15 , TYR A:58 , MET A:202 , ASP A:333 , ALA A:339 , GLC A:604 , ACI A:606 , GLD A:607 , HOH A:704 , HOH A:705 , HOH A:707 , HOH A:862BINDING SITE FOR RESIDUE GLC A 605
06AC6SOFTWARETYR A:58 , HIS A:107 , MET A:202 , ARG A:234 , ASP A:236 , GLU A:266 , HIS A:332 , ASP A:333 , GLC A:605 , GLD A:607BINDING SITE FOR RESIDUE ACI A 606
07AC7SOFTWAREALA A:237 , LYS A:239 , HIS A:240 , GLU A:266 , GLC A:605 , ACI A:606 , GLC A:608 , HOH A:906BINDING SITE FOR RESIDUE GLD A 607
08AC8SOFTWAREGLU A:194 , TYR A:198 , LYS A:239 , LEU A:340 , GLD A:607 , GAL A:609 , HOH A:906 , HOH A:986BINDING SITE FOR RESIDUE GLC A 608
09AC9SOFTWAREGLU A:194 , LYS A:269 , ASN A:270 , GLC A:608 , HOH A:979BINDING SITE FOR RESIDUE GAL A 609
10BC1SOFTWAREGLU A:194 , ASN A:195 , TRP A:284 , GLC A:612 , HOH A:938BINDING SITE FOR RESIDUE GLC A 611
11BC2SOFTWAREASN A:125 , TRP A:284 , HIS A:321 , SER A:323 , HIS A:324 , GLC A:611 , HOH A:939BINDING SITE FOR RESIDUE GLC A 612
12BC3SOFTWAREHIS A:183 , GLU A:391 , GLC A:622BINDING SITE FOR RESIDUE GLC A 621
13BC4SOFTWARETYR A:160 , HIS A:210 , GLU A:212 , GLC A:621BINDING SITE FOR RESIDUE GLC A 622
14BC5SOFTWAREASP A:163 , ALA A:186 , ASP A:188 , ASP A:207 , ASP A:209 , HOH A:711BINDING SITE FOR RESIDUE CA A 501
15BC6SOFTWAREASN A:106 , ASP A:199 , ASP A:205 , HIS A:240 , HOH A:719BINDING SITE FOR RESIDUE CA A 502
16BC7SOFTWAREGLY A:305 , TYR A:307 , HIS A:408 , ASN A:409 , ASP A:432 , HOH A:731BINDING SITE FOR RESIDUE CA A 503
17BC8SOFTWAREASP A:163 , ASP A:188 , ASP A:199 , ASP A:205 , ILE A:206BINDING SITE FOR RESIDUE NA A 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:189 -Glu A:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WPC)

(-) Sequences/Alignments

Asymmetric/Biological 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:481
 aligned with AMT6_BACS7 | P19571 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:481
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517 
           AMT6_BACS7    38 TNGTMMQYFEWYLPNDGNHWNRLNSDASNLKSKGITAVWIPPAWKGASQNDVGYGAYDLYDLGEFNQKGTVRTKYGTRSQLQAAVTSLKNNGIQVYGDVVMNHKGGADATEMVRAVEVNPNNRNQEVTGEYTIEAWTRFDFPGRGNTHSSFKWRWYHFDGVDWDQSRRLNNRIYKFRGHGKAWDWEVDTENGNYDYLMYADIDMDHPEVVNELRNWGVWYTNTLGLDGFRIDAVKHIKYSFTRDWINHVRSATGKNMFAVAEFWKNDLGAIENYLQKTNWNHSVFDVPLHYNLYNASKSGGNYDMRNIFNGTVVQRHPSHAVTFVDNHDSQPEEALESFVEEWFKPLAYALTLTREQGYPSVFYGDYYGIPTHGVPAMRSKIDPILEARQKYAYGKQNDYLDHHNIIGWTREGNTAHPNSGLATIMSDGAGGSKWMFVGRNKAGQVWSDITGNRTGTVTINADGWGNFSVNGGSVSIWVNK 518
               SCOP domains d1wpca2 A:5-398 Bacterial alpha-amylase                                                                                                                                                                                                                                                                                                                                                                   d1wpca1 A:399-485 Bacterial alpha-Amylase                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------Alpha-amylase-1wpcA02 A:24-380                                                                                                                                                                                                                                                                                                                                       ---------------------------------------------DUF1939-1wpcA01 A:426-483                                 -- Pfam domains
         Sec.struct. author ....eee..........hhhhhhhhhhhhhhhhh..eeee....ee.........eee..................hhhhhhhhhhhhhhh..eeeeee...ee....eeeeeeeeeee..eeeee....eeeeeeee...............hhh.eeee...........eeee.......................eee...hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh....eeehhhhhhhhhhhhh.....hhhhh...hhhhhh...eee....................hhhhhhhhhhh....eeeeehhhhhhhhhhh...hhhhhhhhhhhhhhh....eeee.....eeeeee..........eeeeee....eeeeee.hhhhh..eeee.......eee.....eeeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wpc A   5 TNGTMMQYFEWYLPNDGNHWNRLNSDASNLKSKGITAVWIPPAWKGASQNDVGYGAYDLYDLGEFNQKGTVRTKYGTRSQLQAAVTSLKNNGIQVYGDVVMNHKGGADATEMVRAVEVNPNNRNQEVTGEYTIEAWTRFDFPGRGNTHSSFKWRWYHFDGVDWDQSRRLNNRIYKFRGHGKAWDWEVDTENGNYDYLMYADIDMDHPEVVNELRNWGVWYTNTLGLDGFRIDAVKHIKYSFTRDWINHVRSATGKNMFAVAEFWKNDLGAIENYLQKTNWNHSVFDVPLHYNLYNASKSGGNYDMRNIFNGTVVQRHPSHAVTFVDNHDSQPEEALESFVEEWFKPLAYALTLTREQGYPSVFYGDYYGIPTHGVPAMRSKIDPILEARQKYAYGKQNDYLDHHNIIGWTREGNTAHPNSGLATIMSDGAGGSKWMFVGRNKAGQVWSDITGNRTGTVTINADGWGNFSVNGGSVSIWVNK 485
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484
   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  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WPC)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMT6_BACS7 | P19571)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0043169    cation binding    Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
    GO:0033927    glucan 1,4-alpha-maltohexaosidase activity    Catalysis of the hydrolysis of (1->4)-alpha-D-glucosidic linkages in amylaceous polysaccharides, to remove successive maltohexaose residues from the non-reducing chain ends.
    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.
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:0005983    starch catabolic process    The chemical reactions and pathways resulting in the breakdown of starch, the most important reserve polysaccharide in plants.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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        AMT6_BACS7 | P19571: 1wp6 2d3l 2d3n 2gjp 2gjr

(-) Related Entries Specified in the PDB File

1wp6 NATIVE STRUCTURE OF MALTOHEXAOSE-PRODUCING AMYLASE