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(-) Description

Title :  FIVE-DOMAIN ALPHA-AMYLASE FROM BACILLUS STEAROTHERMOPHILUS, MALTOSE/ACARBOSE COMPLEX
 
Authors :  Z. Dauter, M. Dauter, A. M. Brzozowski, S. Christensen, T. V. Borchert, L. Beier, K. S. Wilson, G. J. Davies
Date :  25 May 99  (Deposition) - 31 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Amylase, Glycoside Hydrolase, Starch Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Dauter, M. Dauter, A. M. Brzozowski, S. Christensen, T. V. Borchert, L. Beier, K. S. Wilson, G. J. Davies
X-Ray Structure Of Novamyl, The Five-Domain "Maltogenic" Alpha-Amylase From Bacillus Stearothermophilus: Maltose And Acarbose Complexes At 1. 7A Resolution.
Biochemistry V. 38 8385 1999
PubMed-ID: 10387084  |  Reference-DOI: 10.1021/BI990256L
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE
    Chains: A
    EC Number: 3.2.1.133
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Taxid: 1423
    Fragment: INTACT PROTEIN, ALL 5 DOMAINS
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Other Details: CONTAINS AN ACARBOSE-DERIVED HEXASACCHARIDE AND MALTOSE
    Synonym: "MALTOGENIC" ALPHA AMYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ABD1Ligand/IonACARBOSE DERIVED HEXASACCHARIDE
2CA3Ligand/IonCALCIUM ION
3MAL2Ligand/IonMALTOSE
4SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:612 , LYS A:650 , TRP A:662 , ASN A:667 , HOH A:1523 , HOH A:1892 , HOH A:1934 , HOH A:1939 , HOH A:2256BINDING SITE FOR RESIDUE MAL A 1201
2AC2SOFTWAREASN A:139 , GLN A:412 , ARG A:413 , TRP A:414 , ILE A:415 , SER A:446 , GLY A:447 , HOH A:1289 , HOH A:1426 , HOH A:1695 , HOH A:1756 , HOH A:1834 , HOH A:1845 , HOH A:1905 , HOH A:2012 , HOH A:2181BINDING SITE FOR RESIDUE MAL A 1202
3AC3SOFTWARETYR A:92 , TRP A:93 , HIS A:132 , PHE A:188 , THR A:189 , ASP A:190 , PRO A:191 , ARG A:226 , ASP A:228 , ALA A:229 , LYS A:231 , HIS A:232 , GLU A:256 , TYR A:258 , GLY A:259 , ASP A:260 , ASP A:261 , HIS A:328 , ASP A:329 , ASP A:372 , ARG A:376 , HOH A:1258 , HOH A:1259 , HOH A:1338 , HOH A:1353 , HOH A:1427 , HOH A:1457 , HOH A:1485 , HOH A:1559 , HOH A:1849 , HOH A:2066 , HOH A:2226 , HOH A:2298 , HOH A:2301BINDING SITE FOR RESIDUE ABD A 1200
4AC4SOFTWARESER A:495 , ALA A:496 , LYS A:520 , GLY A:521 , SER A:543 , ASN A:544 , HOH A:1675 , HOH A:2101 , HOH A:2172BINDING SITE FOR RESIDUE SO4 A 1203
5AC5SOFTWAREASP A:76 , ASN A:77 , ASP A:79 , GLU A:101 , GLU A:102 , HOH A:1231BINDING SITE FOR RESIDUE CA A 696
6AC6SOFTWAREASN A:131 , GLN A:184 , ASP A:198 , HIS A:232 , HOH A:1204 , HOH A:1207 , HOH A:1213BINDING SITE FOR RESIDUE CA A 697
7AC7SOFTWAREASP A:21 , ASP A:23 , ASN A:26 , ASN A:27 , GLY A:48 , ASP A:50 , HOH A:1277BINDING SITE FOR RESIDUE CA A 698

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:372 -Pro A:373
2Ala A:505 -Pro A:506
3Gly A:625 -Pro A:626
4Tyr A:632 -Pro A:633

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBM20PS51166 CBM20 (carbohydrate binding type-20) domain profile.AMYM_GEOSE609-719  1A:576-686

(-) Exons   (0, 0)

(no "Exon" information available for 1QHO)

(-) 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:686
 aligned with AMYM_GEOSE | P19531 from UniProtKB/Swiss-Prot  Length:719

    Alignment length:686
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713      
           AMYM_GEOSE    34 SSSASVKGDVIYQIIIDRFYDGDTTNNNPAKSYGLYDPTKSKWKMYWGGDLEGVRQKLPYLKQLGVTTIWLSPVLDNLDTLAGTDNTGYHGYWTRDFKQIEEHFGNWTTFDTLVNDAHQNGIKVIVDFVPNHSTPFKANDSTFAEGGALYNNGTYMGNYFDDATKGYFHHNGDISNWDDRYEAQWKNFTDPAGFSLADLSQENGTIAQYLTDAAVQLVAHGADGLRIDAVKHFNSGFSKSLADKLYQKKDIFLVGEWYGDDPGTANHLEKVRYANNSGVNVLDFDLNTVIRNVFGTFTQTMYDLNNMVNQTGNEYKYKENLITFIDNHDMSRFLSVNSNKANLHQALAFILTSRGTPSIYYGTEQYMAGGNDPYNRGMMPAFDTTTTAFKEVSTLAGLRRNNAAIQYGTTTQRWINNDVYIYERKFFNDVVLVAINRNTQSSYSISGLQTALPNGSYADYLSGLLGGNGISVSNGSVASFTLAPGAVSVWQYSTSASAPQIGSVAPNMGIPGNVVTIDGKGFGTTQGTVTFGGVTATVKSWTSNRIEVYVPNMAAGLTDVKVTAGGVSSNLYSYNILSGTQTSVVFTVKSAPPTNLGDKIYLTGNIPELGNWSTDTSGAVNNAQGPLLAPNYPDWFYVFSVPAGKTIQFKFFIKRADGTIQWENGSNHVATTPTGATGNITVTWQN 719
               SCOP domains d1qhoa4 A:1-407 Cyclodextrin glycosyltransferase                                                                                                                                                                                                                                                                                                                                                                       d1qhoa3 A:408-495 Cyclodextrin glycosyltransferase                                      d1qhoa1 A:496-576                                                                d1qhoa2 A:577-686 Cyclodextrin glycosyltransferase, C-terminal domain                                          SCOP domains
               CATH domains 1qhoA01 A:1-401 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                     1qhoA02 A:402-495 Golgi alpha-mannosidase II                                                  1qhoA03 A:496-577 Immunoglobulins                                                 1qhoA04 A:578-685 Immunoglobulins                                                                           - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee.hhh.....hhh...hhh..................hhhhhhhhhhhhhh...eeee...................................hhhhhhhhhhhhhh..eeeeee....................eee..eeee......................hhhhhh..................hhhhhhhhhhhhhhhh....eeee..hhh..hhhhhhhhhhhhhh...eeee...........hhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhhh...hhh............hhhh...hhhhhhhhhhhhh.....eee..hhh.....................hhhhhhhhhhhhhhh.hhhhh.eeeeeee...eeeeeeee..eeeeeeee......eee.........eee............eee.......eee....eeeeee.......eeeeee........eeeeeee.......eeee......eeee...eeeee......eeeeeeee........eeeee....eeeeeeeee.........eeeeee..hhh.........................eeeeeeee...eeeeeeeee.....eee.....eeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBM20  PDB: A:576-686 UniProt: 609-719                                                                          PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qho A   1 SSSASVKGDVIYQIIIDRFYDGDTTNNNPAKSYGLYDPTKSKWKMYWGGDLEGVRQKLPYLKQLGVTTIWLSPVLDNLDTLAGTDNTGYHGYWTRDFKQIEEHFGNWTTFDTLVNDAHQNGIKVIVDFVPNHSTPFKANDSTFAEGGALYNNGTYMGNYFDDATKGYFHHNGDISNWDDRYEAQWKNFTDPAGFSLADLSQENGTIAQYLTDAAVQLVAHGADGLRIDAVKHFNSGFSKSLADKLYQKKDIFLVGEWYGDDPGTANHLEKVRYANNSGVNVLDFDLNTVIRNVFGTFTQTMYDLNNMVNQTGNEYKYKENLITFIDNHDMSRFLSVNSNKANLHQALAFILTSRGTPSIYYGTEQYMAGGNDPYNRGMMPAFDTTTTAFKEVSTLAGLRRNNAAIQYGTTTQRWINNDVYIYERKFFNDVVLVAINRNTQSSYSISGLQTALPNGSYADYLSGLLGGNGISVSNGSVASFTLAPGAVSVWQYSTSASAPQIGSVAPNMGIPGNVVTIDGKGFGTTQGTVTFGGVTATVKSWTSNRIEVYVPNMAAGLTDVKVTAGGVSSNLYSYNILSGTQTSVVFTVKSAPPTNLGDKIYLTGNIPELGNWSTDTSGAVNNAQGPLLAPNYPDWFYVFSVPAGKTIQFKFFIKRADGTIQWENGSNHVATTPTGATGNITVTWQN 686
                                    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       590       600       610       620       630       640       650       660       670       680
   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  (4, 4)

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

(-) CATH Domains  (3, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QHO)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMYM_GEOSE | P19531)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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:0043897    glucan 1,4-alpha-maltohydrolase activity    Catalysis of the hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive alpha-maltose residues from the non-reducing ends of the chains.
    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.
    GO:2001070    starch binding    Interacting selectively and non-covalently with starch.
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
        AMYM_GEOSE | P19531: 1qhp

(-) Related Entries Specified in the PDB File

1qhp