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(-) Description

Title :  CPOGA D298N IN COMPLEX WITH HOGA-DERIVED O-GLCNAC PEPTIDE
 
Authors :  M. Schimpl, V. S. Borodkin, L. J. Gray, D. M. F. Van Aalten
Date :  24 Mar 11  (Deposition) - 14 Mar 12  (Release) - 14 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,T
Keywords :  Hydrolase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Schimpl, V. S. Borodkin, L. J. Gray, D. M. F. Van Aalten
Synergy Of Peptide And Sugar In O-Glcnacase Substrate Recognition.
Chem. Biol. V. 19 173 2012
PubMed-ID: 22365600  |  Reference-DOI: 10.1016/J.CHEMBIOL.2012.01.011

(-) Compounds

Molecule 1 - O-GLCNACASE NAGJ
    Chains: A
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 31-618
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502
    Synonym: O-GLCNACASE, CPNAGJ, BETA-N-ACETYLHEXOSAMINIDASE, GH84, BETA-HEXOSAMINIDASE, HEXOSAMINIDASE B, N-ACETYL-BETA-GLUCOSAMINIDASE
 
Molecule 2 - BIFUNCTIONAL PROTEIN NCOAT
    Chains: T
    EC Number: 3.2.1.169
    Fragment: HOGA O-GLCNAC PEPTIDE, RESIDUES 402-408
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: O-GLCNAC GLYCOSYLATION ON S405
    Synonym: MENINGIOMA-EXPRESSED ANTIGEN 5, NUCLEAR CYTOPLASMIC O-GLCNACASE AND ACETYLTRANSFERASE, PROTEIN O-GLCNACASE, GLYCOSIDE HYDROLASE O-GLCNACASE, HEXOSAMINIDASE C, N-ACETYL-BETA-D-GLUCOSAMINIDASE, N-ACETYL-BETA-GLUCOSAMINIDASE, O-GLCNACASE, OGA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric/Biological Unit (2, 20)
No.NameCountTypeFull Name
1CD19Ligand/IonCADMIUM ION
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:117 , GLU A:145 , GLU A:545 , HOH A:2022 , HOH A:2025BINDING SITE FOR RESIDUE CD A1620
02AC2SOFTWAREASP A:139 , ASP A:268 , HOH A:2031 , HOH A:2055BINDING SITE FOR RESIDUE CD A1621
03AC3SOFTWAREGLU A:282 , ASP A:286 , GLU A:588 , HOH A:2059 , HOH A:2101BINDING SITE FOR RESIDUE CD A1622
04AC4SOFTWAREASP A:58 , GLU A:272 , HOH A:2007 , HOH A:2008BINDING SITE FOR RESIDUE CD A1623
05AC5SOFTWAREGLU A:54 , ASP A:266 , LYS A:306BINDING SITE FOR RESIDUE CD A1624
06AC6SOFTWAREASP A:112 , GLU A:550 , HOH A:2020 , HOH A:2097 , HOH A:2098BINDING SITE FOR RESIDUE CD A1625
07AC7SOFTWAREGLU A:271 , ARG A:313 , GLU A:581BINDING SITE FOR RESIDUE CD A1626
08AC8SOFTWARELEU A:68 , GLU A:71 , HOH A:2012 , HOH A:2014BINDING SITE FOR RESIDUE CD A1627
09AC9SOFTWAREGLU A:73 , GLU A:108 , ASP A:111 , HOH A:2015 , HOH A:2019BINDING SITE FOR RESIDUE CD A1628
10BC1SOFTWAREASP A:150 , ASP A:252 , HOH A:2032 , HOH A:2033BINDING SITE FOR RESIDUE CD A1629
11BC2SOFTWAREGLU A:170 , HOH A:2010 , HOH A:2011 , HOH A:2030BINDING SITE FOR RESIDUE CD A1630
12BC3SOFTWAREGLU A:362 , ASP A:424 , HOH A:2073 , HOH A:2081BINDING SITE FOR RESIDUE CD A1631
13BC4SOFTWAREGLU A:51 , ASN A:450 , ASP A:452 , HOH A:2086BINDING SITE FOR RESIDUE CD A1632
14BC5SOFTWAREASP A:474 , ARG A:531 , GLU A:534BINDING SITE FOR RESIDUE CD A1633
15BC6SOFTWAREGLU A:272 , HIS A:276BINDING SITE FOR RESIDUE CD A1634
16BC7SOFTWAREHIS A:413BINDING SITE FOR RESIDUE CD A1635
17BC8SOFTWARELYS A:404 , HIS A:433 , HOH A:2075BINDING SITE FOR RESIDUE CD A1636
18BC9SOFTWAREASP A:117 , GLU A:545 , GLU A:549BINDING SITE FOR RESIDUE CD A1637
19CC1SOFTWAREHIS T:404BINDING SITE FOR RESIDUE CD T1409
20CC2SOFTWAREGLY A:187 , PHE A:188 , TYR A:189 , LYS A:218 , ASP A:297 , ASN A:298 , TYR A:335 , THR A:366 , VAL A:370 , TRP A:394 , ASN A:396 , ASP A:401 , ASN A:429 , SER T:405BINDING SITE FOR MONO-SACCHARIDE NAG T 500 BOUND TO SER T 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:47 -Pro A:48
2Tyr A:397 -Pro A:398

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YDQ)

(-) 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:579
 aligned with OGA_CLOP1 | Q0TR53 from UniProtKB/Swiss-Prot  Length:1001

    Alignment length:579
                                    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         
            OGA_CLOP1    40 QVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITVPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYNRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALS 618
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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..........hhhhhhhhhhhh...eeeee......................hhhh.eeeeee....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhh....ee.....ee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ydq A  40 QVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDNIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITVPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYDRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALS 618
                                    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         


Chain T from PDB  Type:PROTEIN  Length:7
 aligned with OGA_HUMAN | O60502 from UniProtKB/Swiss-Prot  Length:916

    Alignment length:7
            OGA_HUMAN   402 VAHSGAK 408
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 2ydq T 402 VAHSGAK 408
   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 2YDQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

Chain T   (OGA_HUMAN | O60502)
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:0004415    hyalurononglucosaminidase activity    Catalysis of the random hydrolysis of (1->4) linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate.
    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:0006044    N-acetylglucosamine metabolic process    The chemical reactions and pathways involving N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.
    GO:0006516    glycoprotein catabolic process    The chemical reactions and pathways resulting in the breakdown of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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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 2xpk 2ydr 2yds 4zxl
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(-) 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
2xpk CELL-PENETRANT, NANOMOLAR O-GLCNACASE INHIBITORS SELECTIVE AGAINST LYSOSOMAL HEXOSAMINIDASES
2ydr CPOGA D298N IN COMPLEX WITH P53-DERIVED O-GLCNAC PEPTIDE
2yds CPOGA D298N IN COMPLEX WITH TAB1-DERIVED O-GLCNAC PEPTIDE