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(-) Description

Title :  BACTEROIDES THETAIOTAOMICRON GH84 O-GLCNACASE IN COMPLEX WITH A IMIDAZOLE-PUGNAC HYBRID INHIBITOR
 
Authors :  R. J. Dennis, G. J. Davies
Date :  25 Aug 06  (Deposition) - 03 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A
Keywords :  Inhibitor, O-Glcnacase, Imidazole, Gh84, Pugnac, Enzyme, Inhibition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Shanmugasundaram, A. W. Debowski, R. J. Dennis, G. J. Davies, D. J. Vocadlo, A. Vasella
Inhibition Of O-Glcnacase By A Gluco-Configured Nagstatin And A Pugnac-Imidazole Hybrid Inhibitor
Chem. Commun. V. 42 4372 2006
PubMed-ID: 17057847  |  Reference-DOI: 10.1039/B612154C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSAMINIDASE
    Atcc: 29148
    Chains: A
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 22-737
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Other Details: PUGNAC-IMIDAZOLE HYBRID INHIBITOR
    Strain: VPI-5482
    Synonym: O-GLCNACASE

 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
1GDV1Ligand/Ion(5R,6R,7R,8S)-8-(ACETYLAMINO)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-N-PHENYL-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-2-CARBOXAMIDE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:135 , PHE A:136 , LYS A:166 , ASP A:242 , ASP A:243 , TYR A:282 , TRP A:286 , ASN A:288 , VAL A:314 , TRP A:337 , ASN A:339 , ASP A:344 , TYR A:345 , ASN A:372 , HIS A:433 , HOH A:2167 , HOH A:2318BINDING SITE FOR RESIDUE GDV A1590
2AC2SOFTWARETYR A:137 , ASP A:344 , TYR A:345 , ARG A:347 , TYR A:550 , GLN A:551 , HOH A:2319BINDING SITE FOR RESIDUE GOL A1719

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J47)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gln A:6 -Pro A:7
2Ala A:173 -Pro A:174
3Phe A:340 -Pro A:341

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J47)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J47)

(-) Exons   (0, 0)

(no "Exon" information available for 2J47)

(-) 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:572
 aligned with OGA_BACTN | Q89ZI2 from UniProtKB/Swiss-Prot  Length:737

    Alignment length:586
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604      
            OGA_BACTN    25 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTD 610
               SCOP domains d2j47a3 A:4-126 G    lucosaminidase GH84, N-      terminal domain                                                          d2j47a2 A:127-436 Glucosaminidase GH84, catalytic domain                                                                                                                                                                                                                                                              d2j47a1 A:437-589 G    lucosaminidase GH84 post-catalytic domain                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee.----.eee.....hhhhhhhhhhhh..------..eeeeee..hhhhhhhh.........eeeee...eeeeee.hhhhhhhhhhhhhhhh....eeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee.................hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh....hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhh----.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j47 A   4 SLQPPPQQLIVQNKTID----YQLNGGEEANPHAVKVLKELLSG------GMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFK----YDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTD 589
                                    13      |  - |      33        43   |     -|       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      
                                           20   25                    47     54                                                                                                                                                                                                                                                                                                                                                                                                              455  460
   Legend:   → Mismatch (orange background)
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  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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J47)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J47)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (OGA_BACTN | Q89ZI2)
molecular function
    GO:0016231    beta-N-acetylglucosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides.
    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: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.
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:0006517    protein deglycosylation    The removal of sugar residues from a glycosylated protein.

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  2j47
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  3.2.1.52
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 Related Entries

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

UniProtKB/Swiss-Prot
        OGA_BACTN | Q89ZI2: 2chn 2cho 2j4g 2jiw 2vvn 2vvs 2w4x 2w66 2w67 2wca 2wzh 2wzi 2x0h 2xj7 2xm1 2xm2 4ais 4aiu 4ur9 5abe 5abf 5abg 5abh 5fky 5fl0 5fl1

(-) Related Entries Specified in the PDB File

2chn BACTEROIDES THETAIOTAOMICRON HEXOSAMINIDASE WITH O-GLCNACASE ACTIVITY
2cho BACTEROIDES THETAIOTAOMICRON HEXOSAMINIDASE WITH O-GLCNACASE ACTIVITY