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(-) Description

Title :  CELL-PENETRANT, NANOMOLAR O-GLCNACASE INHIBITORS SELECTIVE AGAINST LYSOSOMAL HEXOSAMINIDASES
 
Authors :  H. C. Dorfmueller, V. S. Borodkin, M. Schimpl, X. Zheng, R. Kime, K. D. Re D. M. F. Van Aalten
Date :  26 Aug 10  (Deposition) - 16 Mar 11  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Signalling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. C. Dorfmueller, V. S. Borodkin, M. Schimpl, X. Zheng, R. Kime, K. D. Read, D. M. F. Van Aalten
Cell-Penetrant, Nanomolar O-Glcnacase Inhibitors Selective Against Lysosomal Hexosaminidases.
Chem. Biol V. 17 1250 2010
PubMed-ID: 21095575  |  Reference-DOI: 10.1016/J.CHEMBIOL.2010.09.014

(-) Compounds

Molecule 1 - O-GLCNACASE NAGJ
    Chains: A, B
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Fragment: RESIDUES 31-624
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502
    Synonym: BETA-HEXOSAMINIDASE, N-ACETYL-BETA-GLUCOSAMINIDASE, BETA-N- ACETYLHEXOSAMINIDASE, HEXOSAMINIDASE B, GH84, CPOGA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1Z0M2Ligand/IonN-[(5R,6R,7R,8S)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-2-(2-PHENYLETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDIN-8-YL]-3-SULFANYLPROPANAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:187 , PHE A:188 , LYS A:218 , ASP A:297 , ASP A:298 , CYS A:331 , TYR A:335 , THR A:366 , VAL A:370 , ASN A:396 , ASP A:401 , ASN A:429BINDING SITE FOR RESIDUE Z0M A1625
2AC2SOFTWAREASP A:620 , LEU A:623 , GLY B:187 , PHE B:188 , LYS B:218 , ASP B:297 , ASP B:298 , CYS B:331 , TYR B:335 , THR B:366 , VAL B:370 , TRP B:394 , ASN B:396 , ASP B:401 , ASN B:429BINDING SITE FOR RESIDUE Z0M B1625

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gln A:40 -Val A:41
2Asn A:47 -Pro A:48
3Tyr A:397 -Pro A:398
4Val B:41 -Leu B:42
5Asn B:47 -Pro B:48
6Tyr B:397 -Pro B:398

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XPK)

(-) 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:585
 aligned with OGA_CLOP1 | Q0TR53 from UniProtKB/Swiss-Prot  Length:1001

    Alignment length:585
                                    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       509       519       529       539       549       559       569       579       589       599       609       619     
            OGA_CLOP1    40 QVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITVPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYNRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI 624
               SCOP domains d2xpka1 A:40-178 automated matches                                                                                                         d2xpka2 A:179-495 automated matches                                                                                                                                                                                                                                                                                          d2xpka3 A:496-624 automated matches                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee....ee...eeeee.....hhhhhhhhhhhhhhh..ee.........eeeeee....hhhhhhhhh...........eeeeee..eeeeee.hhhhhhhhhhhhhhhh...ee..eeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee................hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhee..eehhhhhhhhhhh....eeee..........hhhhhhhhhhhhh..eeeee......................hhhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....ee.....ee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xpk A  40 QVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITCPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYDRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI 624
                                    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       509       519       529       539       549       559       569       579       589       599       609       619     


Chain B from PDB  Type:PROTEIN  Length:585
 aligned with OGA_CLOP1 | Q0TR53 from UniProtKB/Swiss-Prot  Length:1001

    Alignment length:585
                                    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       509       519       529       539       549       559       569       579       589       599       609       619     
            OGA_CLOP1    40 QVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITVPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYNRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI 624
               SCOP domains d2xpkb1 B:40-178 automated matches                                                                                                         d2xpkb2 B:179-495 automated matches                                                                                                                                                                                                                                                                                          d2xpkb3 B:496-624 automated matches                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------Glyco_hydro_20b-2xpkB03 B:118-177                           ----NAGidase-2xpkB01 B:182-482                                                                                                                                                                                                                                                                                   ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------Glyco_hydro_20b-2xpkB04 B:118-177                           ----NAGidase-2xpkB02 B:182-482                                                                                                                                                                                                                                                                                   ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ............eeee....ee...eeeee.....hhhhhhhhhhhhhhh..ee........eeeeeee....hhhhhhhhh...........eeeeee..eeeeee.hhhhhhhhhhhhhhhh...ee..eeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee................hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhee..eehhhhhhhhhhh....eeee..........hhhhhhhhhhhh...eeeee......................hhhh.eeeeee.......hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhh....ee.....ee....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xpk B  40 QVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITCPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYDRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI 624
                                    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       509       519       529       539       549       559       569       579       589       599       609       619
   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  (3, 6)

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 2XPK)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)
(-)
Clan: no clan defined [family: Glyco_hydro_20b] (22)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (OGA_CLOP1 | Q0TR53)
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: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.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        OGA_CLOP1 | Q0TR53: 2cbi 2cbj 2j1a 2j1e 2j62 2j7m 2jh2 2o4e 2ozn 2v5c 2v5d 2vur 2w1n 2wb5 2x0y 2ydq 2ydr 2yds 4zxl

(-) Related Entries Specified in the PDB File

2cbi STRUCTURE OF THE CLOSTRIDIUM PERFRINGENS NAGJ FAMILY 84 GLYCOSIDE HYDROLASE, A HOMOLOGUE OF HUMAN O-GLCNACASE
2cbj STRUCTURE OF THE CLOSTRIDIUM PERFRINGENS NAGJ FAMILY 84 GLYCOSIDE HYDROLASE, A HOMOLOGUE OF HUMAN O-GLCNACASE IN COMPLEX WITH PUGNAC
2j62 STRUCTURE OF A BACTERIAL O-GLCNACASE IN COMPLEX WITH GLCNACSTATIN
2jh2 X-RAY CRYSTAL STRUCTURE OF A COHESIN-LIKE MODULE FROM CLOSTRIDIUM PERFRINGENS
2v5c FAMILY 84 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS, 2.1 ANGSTROM STRUCTURE
2v5d STRUCTURE OF A FAMILY 84 GLYCOSIDE HYDROLASE AND A FAMILY 32 CARBOHYDRATE-BINDING MODULE IN TANDEM FROM CLOSTRIDIUM PERFRINGENS .
2vur CHEMICAL DISSECTION OF THE LINK BETWEEN STREPTOZOTOCIN, O- GLCNAC AND PANCREATIC CELL DEATH
2wb5 GLCNACSTATINS ARE NANOMOLAR INHIBITORS OF HUMAN O-GLCNACASE INDUCING CELLULAR HYPER-O -GLCNACYLATION
2x0y SCREENING-BASED DISCOVERY OF DRUG-LIKE O- GLCNACASE INHIBITOR SCAFFOLDS