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(-) Description

Title :  X-RAY STRUCTURE OF THE MUTANT OF GLYCOSIDE HYDROLASE
 
Authors :  K. Ishikawa, M. Kataoka, T. Yanamoto, M. Nakabayashi, M. Watanabe
Date :  13 Mar 15  (Deposition) - 29 Apr 15  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycoside Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ishikawa, M. Kataoka, T. Yanamoto, M. Nakabayashi, M. Watanabe, S. Ishihara, S. Yamaguchi
Crystal Structure Of Beta-Galactosidase From Bacillus Circulans Atcc 31382 (Bgad) And The Construction Of The Thermophilic Mutants.
Febs J. V. 282 2540 2015
PubMed-ID: 25879162  |  Reference-DOI: 10.1111/FEBS.13298

(-) Compounds

Molecule 1 - BETA GALACTOSIDASE
    Atcc: 31382
    Chains: A, B
    EC Number: 3.2.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 38-847
    Gene: BGA
    Mutation: YES
    Organism Scientific: BACILLUS CIRCULANS
    Organism Taxid: 1397

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4YPJ)

(-) Sites  (0, 0)

(no "Site" information available for 4YPJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YPJ)

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Leu A:81 -Pro A:82
2Tyr A:134 -Met A:135
3Gln A:181 -Pro A:182
4Thr A:378 -His A:379
5Trp A:593 -Thr A:594
6Thr A:603 -Pro A:604
7Tyr A:609 -Pro A:610
8Leu A:645 -Pro A:646
9Leu B:81 -Pro B:82
10Tyr B:134 -Met B:135
11Gln B:181 -Pro B:182
12Thr B:378 -His B:379
13Trp B:593 -Thr B:594
14Thr B:603 -Pro B:604
15Tyr B:609 -Pro B:610
16Leu B:645 -Pro B:646

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YPJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YPJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4YPJ)

(-) 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:810
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee....eeeee...................eee.....hhhhh.................eeeeeeeee..hhhhh..eeeeee......eeeee..eeeeee......eeee...........eeeeeeeee................eeeeee..eeeeeeeeeee..hhhhhh...eeeeeeeeeeee.....eeeeeeeeee.....eeeeee...eee...eeeeeeeeeeee............eeeeeeeee..eeeeeeeeee....eeee...eeee..ee..eeeeee...hhhhh...hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh.eeeee............hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhhh.eeeee.hhhhhhhhhhhh....eeeeeee...............ee..............ee.....hhhhhhhhhhh...eeeeeee................................hhhhhhhhhhhh....eeee.........eeeeeeee...eeeeee..eeeeeee.eeee.....eeee.......eeeeee....eeeeeee.....eeeeeeee....eeeeeeee...eee.....eeeeeeeeee...........eeeeeeee.eeeeeee.............eee....eeeeeeee....eeeeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ypj A  38 SVSYDGERRVNFNENWRFQRETNGSIAGAQNPGFDDSSWRKLNLPHDWSIELDFNKNSLATHEGGYLDGGIGWYRKTFTIPESMKGKRISLDFDGVYMNSTTYLNGEVLGTYPFGYNAFSYDISDKLYKDGRANVLVVKVNNTQPSSRWYSGSGIYRNVYLTVTDPIHVARYGTFVTTPNLEKSIKEDRADVNIKTKISNDAAEAKQVKIKSTIYDGAGNTVQTVETEEKTAAAGTVTPFEQNTVIKQPKLWSIDKPYRYNLVTEVIVGGQTVDTYETKFGVRYFKFDENEGFSLNGEYMKLHGVSMHHDLGALGAATNARGVERQMQIMKDMGVNAIRVTHNPASPELLEAANKLGLFIIEEAFDSWAQSKKPYDYGRFFNAWAEHDIKEMVDRGKNEPAIIMWSIGNEIYDTTNAAGVETARNLVGWVKEIDTTRPTTIGEDKTRGDKVNVTPINSYIKEIFNIVDVVGLNYSENNYDGYHKQNPSWKLYGSETSSATRSRGVYTHPYQYNQSTKYADLQQSSYDNDYVGWGRTAEDAWKYDRDLKHIAGQFIWTGFDYIGEPTPYYNSYPAKSSYFGAVDTAGFPKDIFYYYQSQWKKEPMVHLLPHWNWKEGEKVRVLAYTNASKVELVLNGESLGEKNYDNKQTSWGAPYKETKDGKTYLEWAVPFKPGKLEAVAKDENGKVIARDQVVTAGEPASVRLTADRKVVKADGTDLSFITADIVDSKGIVVPDADHLITFNVTGQGELAGVDNGNASSVERYKDNKRKAFSGKALAIVQSSKLSGKITVHASVAGLSSDSTSVFTVTP 847
                                    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       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847


Chain B from PDB  Type:PROTEIN  Length:810
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee....eeeee...................eee.....hhhhh.................eeeeeeeee..hhhhh..eeeeee......eeeee..eeeeee......eeee...........eeeeeeeee................eeeeee..eeeeeeeeeee..hhhhhh...eeeeeeeeeeee.....eeeeeeeeee.....eeeeee...eee...eeeeeeeeeeee...........eeeeeeeeee..eeeeeeeeeee...eeee...eeee..ee..eeeeee...hhhhh...hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh.eeeee.............hhhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh......eeeee.............hhhhhhhhhhh.eeeee.hhhhhhhhhhhh....eeeeee................ee..............ee.....hhhhhhhhhhh...eeeeee.................................hhhhhhhhhhhh....eeee.........eeeeeeee...eeeeee..eeeeeee.eeee.....eeee.......eeeeee....eeeeeee.....eeeeeeee....eeeeeeee...eee.....eeeeeeeeee...........eeeeeeee.eeeeeee.............eee....eeeeeeee....eeeeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ypj B  38 SVSYDGERRVNFNENWRFQRETNGSIAGAQNPGFDDSSWRKLNLPHDWSIELDFNKNSLATHEGGYLDGGIGWYRKTFTIPESMKGKRISLDFDGVYMNSTTYLNGEVLGTYPFGYNAFSYDISDKLYKDGRANVLVVKVNNTQPSSRWYSGSGIYRNVYLTVTDPIHVARYGTFVTTPNLEKSIKEDRADVNIKTKISNDAAEAKQVKIKSTIYDGAGNTVQTVETEEKTAAAGTVTPFEQNTVIKQPKLWSIDKPYRYNLVTEVIVGGQTVDTYETKFGVRYFKFDENEGFSLNGEYMKLHGVSMHHDLGALGAATNARGVERQMQIMKDMGVNAIRVTHNPASPELLEAANKLGLFIIEEAFDSWAQSKKPYDYGRFFNAWAEHDIKEMVDRGKNEPAIIMWSIGNEIYDTTNAAGVETARNLVGWVKEIDTTRPTTIGEDKTRGDKVNVTPINSYIKEIFNIVDVVGLNYSENNYDGYHKQNPSWKLYGSETSSATRSRGVYTHPYQYNQSTKYADLQQSSYDNDYVGWGRTAEDAWKYDRDLKHIAGQFIWTGFDYIGEPTPYYNSYPAKSSYFGAVDTAGFPKDIFYYYQSQWKKEPMVHLLPHWNWKEGEKVRVLAYTNASKVELVLNGESLGEKNYDNKQTSWGAPYKETKDGKTYLEWAVPFKPGKLEAVAKDENGKVIARDQVVTAGEPASVRLTADRKVVKADGTDLSFITADIVDSKGIVVPDADHLITFNVTGQGELAGVDNGNASSVERYKDNKRKAFSGKALAIVQSSKLSGKITVHASVAGLSSDSTSVFTVTP 847
                                    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       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847
   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  (0, 0)

(no "SCOP Domain" information available for 4YPJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YPJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YPJ)

(-) Gene Ontology  (5, 5)

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  Cis Peptide Bonds
    Gln A:181 - Pro A:182   [ RasMol ]  
    Gln B:181 - Pro B:182   [ RasMol ]  
    Leu A:645 - Pro A:646   [ RasMol ]  
    Leu A:81 - Pro A:82   [ RasMol ]  
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