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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF TRIPLE (T47M/Y164E/T328N) /MALTOSE OF BACILLUS CEREUS BETA-AMYLASE AT PH 6.5
 
Authors :  A. Hirata, M. Adachi, S. Utsumi, B. Mikami
Date :  03 Apr 04  (Deposition) - 24 May 05  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha-Barrels, Optimum Ph, T47M/Y164E/T328N, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hirata, M. Adachi, S. Utsumi, B. Mikami
Engineering Of The Ph Optimum Of Bacillus Cereus Beta-Amylase: Conversion Of The Ph Optimum From A Bacterial Type To A Higher-Plant Type
Biochemistry V. 43 12523 2004
PubMed-ID: 15449941  |  Reference-DOI: 10.1021/BI049173H
(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: PET21D
    Expression System Strain: HMS174
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
    Synonym: 1,4-ALPHA-D-GLUCAN MALTOHYDROLASE, GLYCOSIDE HYDROLASE FAMILY 14

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA1Ligand/IonCALCIUM ION
3GLC7Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:16 , ASP A:49 , TRP A:51 , HIS A:89 , ASP A:97 , ARG A:397 , HOH A:535 , HOH A:536 , HOH A:586 , BGC A:901BINDING SITE FOR RESIDUE GLC A 900
2AC2SOFTWAREALA A:170 , GLU A:172 , LYS A:287 , THR A:330 , GLU A:367 , ALA A:369 , HOH A:642 , HOH A:651 , GLC A:900 , GLC A:902BINDING SITE FOR RESIDUE BGC A 901
3AC3SOFTWAREGLU A:172 , ARG A:174 , TYR A:178 , GLY A:290 , HIS A:292 , THR A:330 , CYS A:331 , HOH A:586 , BGC A:901 , GLC A:903BINDING SITE FOR RESIDUE GLC A 902
4AC4SOFTWAREVAL A:95 , TYR A:186 , HIS A:292 , LEU A:370 , HOH A:604 , GLC A:902BINDING SITE FOR RESIDUE GLC A 903
5AC5SOFTWARETRP A:221 , ALA A:230 , ILE A:231 , LEU A:232 , PRO A:233 , SER A:235 , TYR A:249 , HOH A:584 , HOH A:683 , GLC A:905BINDING SITE FOR RESIDUE GLC A 904
6AC6SOFTWARETHR A:223 , PRO A:234 , GLN A:239 , PHE A:240 , GLY A:244 , TYR A:249 , HOH A:569 , GLC A:904BINDING SITE FOR RESIDUE GLC A 905
7AC7SOFTWARETRP A:449 , LYS A:482 , GLN A:499 , GLC A:907BINDING SITE FOR RESIDUE GLC A 906
8AC8SOFTWARELYS A:482 , TRP A:495 , GLC A:906BINDING SITE FOR RESIDUE GLC A 907
9AC9SOFTWAREGLU A:56 , ASP A:60 , GLN A:61 , GLU A:141 , GLU A:144 , HOH A:757BINDING SITE FOR RESIDUE CA A 930

(-) 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 1VEP)

(-) 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 1VEP)

(-) 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 d1vepa2 A:1-417 automated matches                                                                                                                                                                                                                                                                                                                                                                                                d1vepa1 A:418-516 automated matches                                                                 SCOP domains
               CATH domains 1vepA01 A:1-416 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                    1vepA02 A:417-516 Immunoglobulins                                                                    CATH domains
               Pfam domains -------------Glyco_hydro_14-1vepA02 A:14-413                                                                                                                                                                                                                                                                                                                                                                                 -----CBM_20-1vepA01 A:419-515                                                                         - Pfam domains
         Sec.struct. author hhhhh......eeeee....hhhhh.hhhhhhhhhhhhhhh.eeeeeeeeehhhhh........hhhhhhhhhhhhhh..eeeeeee................hhhhhhhh......ee.....ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee................hhhhhh..hhhhhhhhhhhhh.eeee...............hhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh...eeeeeeeee........eeeeee.hhhhh........ee.eee....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
                 1vep A   1 AVNGKGMNPDYKAYLMAPLKKIPEVTNWETFENDLRWAKQNGFYAIMVDFWWGDMEKNGDQQFDFSYAQRFAQSVKNAGMKMIPIISTHQCGGNVGDDCNVPIPSWVWNQKSDDSLYFKSETGTVNKETLNPLASDVIRKEYGELYTAFAAAMKPYKDVIAKIELSGGPAGELRYPSYTTSDGTGYPSRGKFQAYTEFAKSKFRLWVLNKYGSLNEVNKAWGTKLISELAILPPSDGEQFLMNGYLSMYGKDYLEWYQGILENHTKLIGELAHNAFDTTFQVPIGAKIAGVHWQYNNPTIPHGAEKPAGYNDYSHLLDAFKSAKLDVNFTCLEMTDKGSYPEYSMPKTLVQNIATLANEKGIVLNGENALSIGNEEEYKRVAEMAFNYNFAGFTLLRYQDVMYNNSLMGKFKDLLGVTPVMQTIVVKNVPTTIGDTVYITGNRAELGSWDTKQYPIQLYYDSHSNDWRGNVVLPAERNIEFKAFIKSKDGTVKSWQTIQQSWNPVPLKTTSHTSSW 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  (2, 2)

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

(-) 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 1itc 1j0y 1j0z 1j10 1j11 1j12 1j18 1vem 1ven 1veo 5bca

(-) Related Entries Specified in the PDB File

1vem BETA-AMYLASE AT THE OPTIMUM PH 6.5
1ven Y164E/MALTOSE OF BACILUS CEREUS BETA-AMYLASE AT PH 4.6
1veo Y164F/MALTOSE OF BACILLUS CEREUS BETA-AMYLASE AT PH 4.6