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(-) Description

Title :  THE COHESIN-DOCKERIN COMPLEX OF NAGJ AND NAGH FROM CLOSTRIDIUM PERFRINGENS
 
Authors :  J. J. Adams, A. Boraston, S. P. Smith
Date :  26 Feb 07  (Deposition) - 06 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ef Hand, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. J. Adams, K. Gregg, E. A. Bayer, A. B. Boraston, S. P. Smith
Structural Basis Of Clostridium Perfringens Toxin Complex Formation.
Proc. Natl. Acad. Sci. Usa V. 105 12194 2008
PubMed-ID: 18716000  |  Reference-DOI: 10.1073/PNAS.0803154105

(-) Compounds

Molecule 1 - O-GLCNACASE NAGJ
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentCOHESIN MODULE (RESIDUES 768-909)
    GeneNAGJ
    Organism ScientificCLOSTRIDIUM PERFRINGENS
    Organism Taxid195103
    StrainATCC 13124
    SynonymBETA-HEXOSAMINIDASE, N-ACETYL-BETA-GLUCOSAMINIDASE, BETA-N- ACETYLHEXOSAMINIDASE, HEXOSAMINIDASE B, GH84
 
Molecule 2 - HYALURONONGLUCOSAMINIDASE
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentFIVAR-DOCKERIN MODULAR PAIR (RESIDUES 1498-1628)
    GeneNAGH
    Organism ScientificCLOSTRIDIUM PERFRINGENS
    Organism Taxid1502
    StrainSTRAIN 13
    SynonymHYALURONIDASE, MU TOXIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:1607 , ASN B:1609 , ASP B:1611 , SER B:1613 , GLU B:1618 , HOH B:1683BINDING SITE FOR RESIDUE CA B 401
2AC2SOFTWAREASP B:1579 , ASN B:1581 , ASN B:1583 , LYS B:1585 , ASP B:1590 , HOH B:1723BINDING SITE FOR RESIDUE CA B 402
3AC3SOFTWAREASP A:811 , PHE A:812 , THR A:813 , ASN A:882 , HOH A:988BINDING SITE FOR RESIDUE CL A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OZN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DOCKERINPS51766 Dockerin domain profile.NAGH_CLOPE1573-1628  1B:1573-1628

(-) Exons   (0, 0)

(no "Exon" information available for 2OZN)

(-) 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:133
 aligned with OGA_CLOP1 | Q0TR53 from UniProtKB/Swiss-Prot  Length:1001

    Alignment length:133
                                   783       793       803       813       823       833       843       853       863       873       883       893       903   
           OGA_CLOP1    774 EVTGSVSLEALEEVQVGENLEVGVGIDELVNAEAFAYDFTLNYDENAFEYVEAISDDGVFVNAKKIEDGKVRVLVSSLTGEPLPAKEVLAKVVLRAEAKAEGSNLSVTNSSVGDGEGLVHEIAGTEKTVNIIE  906
               SCOP domains d2ozna1 A:774-906 O-GlcNAcase NagJ                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eee...eeeeeeeeeeee.....eeeeeee.....eeeeeee....eeeeeeeee..eeeeeeee..........eeeeeeeee...eeeeeeeeeeeeee.....eee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ozn A  774 EVTGSVSLEALEEVQVGENLEVGVGIDELVNAEAFAYDFTLNYDENAFEYVEAISDDGVFVNAKKIEDGKVRVLVSSLTGEPLPAKEVLAKVVLRAEAKAEGSNLSVTNSSVGDGEGLVHEIAGTEKTVNIIE  906
                                   783       793       803       813       823       833       843       853       863       873       883       893       903   

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with NAGH_CLOPE | P26831 from UniProtKB/Swiss-Prot  Length:1628

    Alignment length:131
                                  1507      1517      1527      1537      1547      1557      1567      1577      1587      1597      1607      1617      1627 
          NAGH_CLOPE   1498 DKTNLGELINQGKSLLDESVEGFNVGEYHKGAKDGLTVEINKAEEVFNKEDATEEEINLAKESLEGAIARFNSLLIEESTGDFNGNGKIDIGDLAMVSKNIGSTTNTSLDLNKDGSIDEYEISFINHRILN 1628
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------FIVAR-2oznB01 B:1505-1557                            ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhh.................hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------DOCKERIN  PDB: B:1573-1628 UniProt: 1573-1628            PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ozn B 1498 DKTNLGELINQGKSLLDESVEGFNVGEYHKGAKDGLTVEINKAEEVFNKEDATEEEINLAKESLEGAIARFNSLLIEESTGDFNGNGKIDIGDLAMVSKNIGSTTNTSLDLNKDGSIDEYEISFINHRILN 1628
                                  1507      1517      1527      1537      1547      1557      1567      1577      1587      1597      1607      1617      1627 

   Legend:   → Mismatch (orange background)
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    → 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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (12, 15)

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 B   (NAGH_CLOPE | P26831)
molecular function
    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: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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NAGH_CLOPE | P268312jnk 2w1q 2w1s 2w1u 2wdb
        OGA_CLOP1 | Q0TR532cbi 2cbj 2j1a 2j1e 2j62 2j7m 2jh2 2o4e 2v5c 2v5d 2vur 2w1n 2wb5 2x0y 2xpk 2ydq 2ydr 2yds 4zxl

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