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(-) Description

Title :  BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES COMPLEXED WITH MALTOPENTAOSE
 
Authors :  H. Miyake, G. Kurisu, M. Kusunoki, S. Nishimura, S. Kitamura, Y. Nitta
Date :  17 Jan 02  (Deposition) - 27 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Beta-Amylase, Raw-Starch Binding Domain, Maltopentaose, Catalytic-Site Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Miyake, G. Kurisu, M. Kusunoki, S. Nishimura, S. Kitamura, Y. Nitta
Crystal Structure Of A Catalytic Site Mutant Of Beta-Amylase From Bacillus Cereus Var. Mycoides Cocrystallized With Maltopentaose
Biochemistry V. 42 5574 2003
PubMed-ID: 12741813  |  Reference-DOI: 10.1021/BI020712X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-AMYLASE
    Chains: A
    EC Number: 3.2.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
    Strain: VAR.MYCOIDES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric/Biological Unit (4, 17)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2CA1Ligand/IonCALCIUM ION
3GLC14Ligand/IonALPHA-D-GLUCOSE
4SO41Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:49 , TRP A:51 , HIS A:89 , ASP A:97 , ARG A:397 , GLC A:602 , HOH A:714 , HOH A:721 , HOH A:750 , HOH A:1051BINDING SITE FOR RESIDUE GLC A 601
02AC2SOFTWAREMET A:16 , VAL A:95 , ALA A:170 , LYS A:287 , GLU A:367 , ALA A:369 , LEU A:396 , GLC A:601 , GLC A:603 , HOH A:728 , HOH A:958 , HOH A:961 , HOH A:1051 , HOH A:1059BINDING SITE FOR RESIDUE GLC A 602
03AC3SOFTWAREALA A:170 , ARG A:174 , TYR A:178 , GLY A:290 , THR A:330 , CYS A:331 , GLC A:602 , GLC A:604 , HOH A:1074BINDING SITE FOR RESIDUE GLC A 603
04AC4SOFTWAREVAL A:95 , TYR A:186 , HIS A:292 , MET A:334 , LEU A:370 , GLC A:603 , GLC A:605 , HOH A:753 , HOH A:995 , HOH A:1084BINDING SITE FOR RESIDUE GLC A 604
05AC5SOFTWARELEU A:370 , GLC A:604BINDING SITE FOR RESIDUE GLC A 605
06AC6SOFTWAREALA A:230 , ILE A:231 , LEU A:232 , PRO A:233 , SER A:235 , TYR A:249 , GLC A:607 , HOH A:807 , HOH A:858BINDING SITE FOR RESIDUE GLC A 606
07AC7SOFTWARETHR A:223 , PHE A:240 , GLY A:244 , TYR A:249 , GLC A:606 , GLC A:608 , HOH A:724 , HOH A:878BINDING SITE FOR RESIDUE GLC A 607
08AC8SOFTWAREASP A:64 , SER A:66 , GLN A:239 , ASN A:243 , GLC A:607 , GLC A:609 , HOH A:1053BINDING SITE FOR RESIDUE GLC A 608
09AC9SOFTWAREASP A:64 , GLN A:239 , GLC A:608BINDING SITE FOR RESIDUE GLC A 609
10BC1SOFTWARETRP A:449 , GLC A:611BINDING SITE FOR RESIDUE GLC A 610
11BC2SOFTWARETRP A:449 , GLN A:499 , GLC A:610 , GLC A:612BINDING SITE FOR RESIDUE GLC A 611
12BC3SOFTWARELYS A:482 , TRP A:495 , GLC A:611 , HOH A:979BINDING SITE FOR RESIDUE GLC A 612
13BC4SOFTWAREGLU A:238 , ASN A:297 , THR A:299 , GLC A:614BINDING SITE FOR RESIDUE GLC A 613
14BC5SOFTWARESER A:188 , ARG A:189 , GLN A:294 , ASN A:297 , ILE A:300 , TYR A:340 , PRO A:341 , TYR A:343 , GLC A:613BINDING SITE FOR RESIDUE GLC A 614
15BC6SOFTWAREGLU A:56 , ASP A:60 , GLU A:141 , GLU A:144 , HOH A:1042BINDING SITE FOR RESIDUE CA A 1500
16BC7SOFTWAREASN A:404 , ASN A:405 , SER A:406 , HOH A:854 , HOH A:889BINDING SITE FOR RESIDUE SO4 A 1501
17BC8SOFTWAREASN A:131 , LEU A:133 , TYR A:175 , GLN A:193 , ALA A:194 , ALA A:199 , HOH A:700BINDING SITE FOR RESIDUE ACY A 1502

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:91 -A:99

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:186 -Pro A:187
2Tyr A:340 -Pro A:341
3Leu A:396 -Arg A:397
4Asn A:503 -Pro A:504

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_AMYLASE_1PS00506 Beta-amylase active site 1.AMYB_BACCE119-127  1A:89-97
2BETA_AMYLASE_2PS00679 Beta-amylase active site 2.AMYB_BACCE198-208  1A:168-178
3CBM20PS51166 CBM20 (carbohydrate binding type-20) domain profile.AMYB_BACCE444-546  1A:414-516

(-) Exons   (0, 0)

(no "Exon" information available for 1ITC)

(-) 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:516
 aligned with AMYB_BACCE | P36924 from UniProtKB/Swiss-Prot  Length:546

    Alignment length:516
                                    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      
           AMYB_BACCE    31 AVNGKGMNPDYKAYLMAPLKKIPEVTNWETFENDLRWAKQNGFYAITVDFWWGDMEKNGDQQFDFSYAQRFAQSVKNAGMKMIPIISTHQCGGNVGDDCNVPIPSWVWNQKSDDSLYFKSETGTVNKETLNPLASDVIRKEYGELYTAFAAAMKPYKDVIAKIYLSGGPAGELRYPSYTTSDGTGYPSRGKFQAYTEFAKSKFRLWVLNKYGSLNEVNKAWGTKLISELAILPPSDGEQFLMNGYLSMYGKDYLEWYQGILENHTKLIGELAHNAFDTTFQVPIGAKIAGVHWQYNNPTIPHGAEKPAGYNDYSHLLDAFKSAKLDVTFTCLEMTDKGSYPEYSMPKTLVQNIATLANEKGIVLNGENALSIGNEEEYKRVAEMAFNYNFAGFTLLRYQDVMYNNSLMGKFKDLLGVTPVMQTIVVKNVPTTIGDTVYITGNRAELGSWDTKQYPIQLYYDSHSNDWRGNVVLPAERNIEFKAFIKSKDGTVKSWQTIQQSWNPVPLKTTSHTSSW 546
               SCOP domains d1itca2 A:1-417 Bacterial beta-amylase                                                                                                                                                                                                                                                                                                                                                                                           d1itca1 A:418-516 beta-amylase                                                                      SCOP domains
               CATH domains 1itcA01 A:1-416 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                    1itcA02 A:417-516 Immunoglobulins                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh......eeeee....hhhhh.hhhhhhhhhhhhhhh.eeeeeeeeehhhhh........hhhhhhhhhhhhhh...eeeeee................hhhhhhhh......ee.....ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee................hhhhhh..hhhhhhhhhhhhh.eeee...............hhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhh...eeeeeeeee........eeeeee.hhhhhhhh.....eeeeee....eeeeeeeee....eeeeeeee.....eeee....eee........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------BETA_AMYL----------------------------------------------------------------------BETA_AMYLAS-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBM20  PDB: A:414-516 UniProt: 444-546                                                                  PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1itc A   1 AVNGKGMNPDYKAYLMAPLKKIPEVTNWETFENDLRWAKQNGFYAITVDFWWGDMEKNGDQQFDFSYAQRFAQSVKNAGMKMIPIISTHQCGGNVGDDCNVPIPSWVWNQKSDDSLYFKSETGTVNKETLNPLASDVIRKEYGELYTAFAAAMKPYKDVIAKIYLSGGPAGALRYPSYTTSDGTGYPSRGKFQAYTEFAKSKFRLWVLNKYGSLNEVNKAWGTKLISELAILPPSDGEQFLMNGYLSMYGKDYLEWYQGILENHTKLIGELAHNAFDTTFQVPIGAKIAGVHWQYNNPTIPHGAEKPAGYNDYSHLLDAFKSAKLDVTFTCLEMTDKGSYPEYSMPKTLVQNIATLANEKGIVLNGENALSIGNEEEYKRVAEMAFNYNFAGFTLLRYQDVMYNNSLMGKFKDLLGVTPVMQTIVVKNVPTTIGDTVYITGNRAELGSWDTKQYPIQLYYDSHSNDWRGNVVLPAERNIEFKAFIKSKDGTVKSWQTIQQSWNPVPLKTTSHTSSW 516
                                    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
   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  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMYB_BACCE | P36924)
molecular function
    GO:0016161    beta-amylase activity    Catalysis of the reaction: (1,4-alpha-D-glucosyl)(n+1) + H2O = (1,4-alpha-D-glucosyl)(n-1) + alpha-maltose. This reaction is the hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides so as to remove successive maltose units 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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0005976    polysaccharide metabolic process    The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMYB_BACCE | P36924: 1b90 1b9z 1cqy 1j0y 1j0z 1j10 1j11 1j12 1j18 1vem 1ven 1veo 1vep 5bca

(-) Related Entries Specified in the PDB File

1itd 1ITD CONTAINS THE SAME PROTEIN, MUTANT E367A COMPLEXED WITH OLIGOSACCHARIDE.
1itj 1ITJ CONTAINS THE SAME PROTEIN COMPLEXED WITH GLUCOSES.
5bca 5BCA CONTAINS THE SAME PROTEIN, WILD TYPE.