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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-HEXOSAMINIDASE FROM PAENIBACILLUS SP. TS12 IN COMPLEX WITH NAG-THIAZOLINE.
 
Authors :  T. Sumida, S. Yokoyama, Riken Structural Genomics/Proteomics Ini (Rsgi)
Date :  11 Jul 11  (Deposition) - 06 Jun 12  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Tim Barrel, Hydrolase, Carbohydrate/Sugar Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Sumida, K. A. Stubbs, M. Ito, S. Yokoyama
Gaining Insight Into The Inhibition Of Glycoside Hydrolase Family 20 Exo-Beta-N-Acetylhexosaminidases Using A Structural Approach
Org. Biomol. Chem. V. 10 2607 2012
PubMed-ID: 22367352  |  Reference-DOI: 10.1039/C2OB06636J

(-) Compounds

Molecule 1 - BETA-HEXOSAMINIDASE
    Chains: A
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HEX1
    Organism Scientific: PAENIBACILLUS
    Organism Taxid: 192895
    Strain: TS12

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NGT1Ligand/Ion3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:106 , SER A:107 , ASN A:108 , ARG A:411 , HOH A:545 , HOH A:579 , HOH A:652 , HOH A:758 , HOH A:785BINDING SITE FOR RESIDUE SO4 A 1500
2AC2SOFTWAREARG A:170 , HIS A:258 , ASP A:321 , GLU A:322 , TRP A:352 , TRP A:370 , TYR A:395 , ASP A:397 , LEU A:408 , TRP A:410 , TRP A:441 , GLU A:443 , HOH A:522BINDING SITE FOR RESIDUE NGT A 2000

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:372 -A:427

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:19 -Pro A:20
2Met A:255 -Pro A:256
3Asp A:353 -Pro A:354
4Tyr A:456 -Pro A:457

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SUR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SUR)

(-) Exons   (0, 0)

(no "Exon" information available for 3SUR)

(-) 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:504
 aligned with D0VX21_PAESP | D0VX21 from UniProtKB/TrEMBL  Length:505

    Alignment length:506
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499      
         D0VX21_PAESP     - -MASMMSFIPESASASTSQPSILPKPVSYTVGSGQFVLTKNASIFVAGNNVGETDELFNIGQALAKKLNASTGYTISVVKSNQPTAGSIYLTTVGGNAALGNEGYDLITTSNQVTLTANKPEGVFRGNQTLLQLLPAGIEKNTVVSGVQWVIPHSNISDKPEYEYRGLMLDVARHFFTVDEVKRQIDLASQYKINKFHMHLSDDQGWRIEIKSWPDLIEIGSKGQVGGGPGGYYTQEQFKDIVSYAAERYIEVIPEIDMPGHTNAALASYGELNPDGKRKAMRTDTAVGYSTLMPRAEITYQFVEDVISELAAISPSPYIHLGGDESNATSAADYDYFFGRVTAIANSYGKKVVGWDPSDTSSGATSDSVLQNWTCSASTGTAAKAKGMKVIVSPANAYLDMKYYSDSPIGLQWRGFVNTNRAYNWDPTDCIKGANIYGVESTLWTETFVTQDHLDYMLYPKLLSNAEVGWTARGDRNWDDFKERLIEHTPRLQNKGIKFFADPIV 505
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............--............eeeeeeeeee......eeee..hhhhhhhhhhhhhhhhhhhhhhhh....eee.......eeeee....hhhhh...eeeee...eeeeee.hhhhhhhhhhhhhhhh...............eeeeeeeee.....eeeeeee......hhhhhhhhhhhhhh....eeeee..............hhhhhh....hhhhh.....hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.......eeee.......hhhhhhhh..eee.hhhhh...........................hhhhhh....eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sur A -16 HHHHSSGLVPRGS--HMSQPSILPKPVSYTVGSGQFVLTKNASIFVAGNNVGETDELFNIGQALAKKLNASTGYTISVVKSNQPTAGSIYLTTVGGNAALGNEGYDLITTSNQVTLTANKPEGVFRGNQTLLQLLPAGIEKNTVVSGVQWVIPHSNISDKPEYEYRGLMLDVARHFFTVDEVKRQIDLASQYKINKFHMHLSDDQGWRIEIKSWPDLIEIGSKGQVGGGPGGYYTQEQFKDIVSYAAERYIEVIPEIDMPGHTNAALASYGELNPDGKRKAMRTDTAVGYSTLMPRAEITYQFVEDVISELAAISPSPYIHLGGDESNATSAADYDYFFGRVTAIANSYGKKVVGWDPSDTSSGATSDSVLQNWTCSASTGTAAKAKGMKVIVSPANAYLDMKYYSDSPIGLQWRGFVNTNRAYNWDPTDCIKGANIYGVESTLWTETFVTQDHLDYMLYPKLLSNAEVGWTARGDRNWDDFKERLIEHTPRLQNKGIKFFADPIV 502
                                    -7  |  |||16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496      
                                       -4 -3||                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                           -2|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                            14                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain A from PDB  Type:PROTEIN  Length:504
 aligned with D2KW09_9BACL | D2KW09 from UniProtKB/TrEMBL  Length:978

    Alignment length:504
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498    
         D2KW09_9BACL     - --MMSFIPESASASTSQPSILPKPVSYTVGSGQFVLTKNASIFVAGNNVGETDELFNIGQALAKKLNASTGYTISVVKSNQPTAGSIYLTTVGGNAALGNEGYDLITTSNQVTLTANKPEGVFRGNQTLLQLLPAGIEKNTVVSGVQWVIPHSNISDKPEYEYRGLMLDVARHFFTVDEVKRQIDLASQYKINKFHMHLSDDQGWRIEIKSWPDLIEIGSKGQVGGGPGGYYTQEQFKDIVSYAAERYIEVIPEIDMPGHTNAALASYGELNPDGKRKAMRTDTAVGYSTLMPRAEITYQFVEDVISELAAISPSPYIHLGGDESNATSAADYDYFFGRVTAIANSYGKKVVGWDPSDTSSGATSDSVLQNWTCSASTGTAAKAKGMKVIVSPANAYLDMKYYSDSPIGLQWRGFVNTNRAYNWDPTDCIKGANIYGVESTLWTETFVTQDHLDYMLYPKLLSNAEVGWTARGDRNWDDFKERLIEHTPRLQNKGIKFFADPIV 502
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........................eeeeeeeeee......eeee..hhhhhhhhhhhhhhhhhhhhhhhh....eee.......eeeee....hhhhh...eeeee...eeeeee.hhhhhhhhhhhhhhhh...............eeeeeeeee.....eeeeeee......hhhhhhhhhhhhhh....eeeee..............hhhhhh....hhhhh.....hhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.......eeee.......hhhhhhhh..eee.hhhhh...........................hhhhhh....eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3sur A -16 HHHHSSGLVPRGSHMSQPSILPKPVSYTVGSGQFVLTKNASIFVAGNNVGETDELFNIGQALAKKLNASTGYTISVVKSNQPTAGSIYLTTVGGNAALGNEGYDLITTSNQVTLTANKPEGVFRGNQTLLQLLPAGIEKNTVVSGVQWVIPHSNISDKPEYEYRGLMLDVARHFFTVDEVKRQIDLASQYKINKFHMHLSDDQGWRIEIKSWPDLIEIGSKGQVGGGPGGYYTQEQFKDIVSYAAERYIEVIPEIDMPGHTNAALASYGELNPDGKRKAMRTDTAVGYSTLMPRAEITYQFVEDVISELAAISPSPYIHLGGDESNATSAADYDYFFGRVTAIANSYGKKVVGWDPSDTSSGATSDSVLQNWTCSASTGTAAKAKGMKVIVSPANAYLDMKYYSDSPIGLQWRGFVNTNRAYNWDPTDCIKGANIYGVESTLWTETFVTQDHLDYMLYPKLLSNAEVGWTARGDRNWDDFKERLIEHTPRLQNKGIKFFADPIV 502
                                    -7    ||  18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498    
                                         -2|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                          14
   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 3SUR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SUR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SUR)

(-) Gene Ontology  (8, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D0VX21_PAESP | D0VX21)
molecular function
    GO:0004563    beta-N-acetylhexosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
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.

Chain A   (D2KW09_9BACL | D2KW09)
molecular function
    GO:0004563    beta-N-acetylhexosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
    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: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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        D0VX21_PAESP | D0VX21: 3sus 3sut 3suu 3suv 3suw
UniProtKB/TrEMBL
        D0VX21_PAESP | D0VX21: 3gh4 3gh5 3gh7
        D2KW09_9BACL | D2KW09: 3sus 3sut 3suu 3suv 3suw

(-) Related Entries Specified in the PDB File

3sus 3sut 3suu 3suv 3suw