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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF A COHESIN-LIKE MODULE FROM CLOSTRIDIUM PERFRINGENS
 
Authors :  S. Chitayat, K. Gregg, J. J. Adams, E. Ficko-Blean, E. A. Bayer, A. B. Bor S. P. Smith
Date :  19 Feb 07  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hydrolase, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chitayat, K. Gregg, J. J. Adams, E. Ficko-Blean, E. A. Bayer, A. B. Boraston, S. P. Smith
Three-Dimensional Structure Of A Putative Non- Cellulosomal Cohesin Module From A Clostridium Perfringens Family 84 Glycoside Hydrolase.
J. Mol. Biol. V. 375 20 2008
PubMed-ID: 17999932  |  Reference-DOI: 10.1016/J.JMB.2007.10.031

(-) Compounds

Molecule 1 - O-GLCNACASE NAGJ
    Atcc: 13124
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 768-909
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502
    Synonym: BETA-HEXOSAMINIDASE, N-ACETYL-BETA-GLUCOSAMINIDASE, BETA-N-ACETYLHEXOSAMINIDASE, HEXOSAMINIDASE B, GH84

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2JH2)

(-) Sites  (0, 0)

(no "Site" information available for 2JH2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JH2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp B:62 -Asp B:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JH2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JH2)

(-) Exons   (0, 0)

(no "Exon" information available for 2JH2)

(-) 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 d2jh2a1 A:7-139 O-GlcNAcase NagJ                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eee...eeeeeeeeeeee.....eeeeeeee....eeeeeeee...eeeeeeeee..eeeeeeee..........eeeeeeeee...eeeeeeeeeeeeee.....eee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jh2 A   7 EVTGSVSLEALEEVQVGENLEVGVGIDELVNAEAFAYDFTLNYDENAFEYVEAISDDGVFVNAKKIEDGKVRVLVSSLTGEPLPAKEVLAKVVLRAEAKAEGSNLSVTNSSVGDGEGLVHEIAGTEKTVNIIE 139
                                    16        26        36        46        56        66        76        86        96       106       116       126       136   


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with OGA_CLOP1 | Q0TR53 from UniProtKB/Swiss-Prot  Length:1001

    Alignment length:134
                                   783       793       803       813       823       833       843       853       863       873       883       893       903    
            OGA_CLOP1   774 EVTGSVSLEALEEVQVGENLEVGVGIDELVNAEAFAYDFTLNYDENAFEYVEAISDDGVFVNAKKIEDGKVRVLVSSLTGEPLPAKEVLAKVVLRAEAKAEGSNLSVTNSSVGDGEGLVHEIAGTEKTVNIIEG 907
               SCOP domains d2jh2b_ B: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eee...eeeeeeeeeeee.....eeeeeeee....eeeeeeee...eeeeeeeee..eeeeeeee..........eeeeeeeee...eeeeeeeeeeeeee.....eeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jh2 B   7 EVTGSVSLEALEEVQVGENLEVGVGIDELVNAEAFAYDFTLNYDENAFEYVEAISDDGVFVNAKKIEDGKVRVLVSSLTGEPLPAKEVLAKVVLRAEAKAEGSNLSVTNSSVGDGEGLVHEIAGTEKTVNIIEG 140
                                    16        26        36        46        56        66        76        86        96       106       116       126       136    


Chain C from PDB  Type:PROTEIN  Length:130
 aligned with OGA_CLOP1 | Q0TR53 from UniProtKB/Swiss-Prot  Length:1001

    Alignment length:130
                                   784       794       804       814       824       834       844       854       864       874       884       894       904
            OGA_CLOP1   775 VTGSVSLEALEEVQVGENLEVGVGIDELVNAEAFAYDFTLNYDENAFEYVEAISDDGVFVNAKKIEDGKVRVLVSSLTGEPLPAKEVLAKVVLRAEAKAEGSNLSVTNSSVGDGEGLVHEIAGTEKTVNI 904
               SCOP domains d2jh2c_ C: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........eeeeeeeeeee......eeeeeee.....eeeeeeee...eeeeeeeee..eeeeeeee..........eeeeeeeee...eeeeeeeeeeeeee.....eeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jh2 C   8 VTGSVSLEALEEVQVGENLEVGVGIDELVNAEAFAYDFTLNYDENAFEYVEAISDDGVFVNAKKIEDGKVRVLVSSLTGEPLPAKEVLAKVVLRAEAKAEGSNLSVTNSSVGDGEGLVHEIAGTEKTVNI 137
                                    17        27        37        47        57        67        77        87        97       107       117       127       137
   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  (2, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JH2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2JH2)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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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  Cis Peptide Bonds
    Asp B:62 - Asp B:63   [ RasMol ]  
 

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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 2o4e 2ozn 2v5c 2v5d 2vur 2w1n 2wb5 2x0y 2xpk 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
2j1a STRUCTURE OF CBM32 FROM CLOSTRIDIUM PERFRINGENS BETA-N-ACETYLHEXOSAMINIDASE GH84C IN COMPLEX WITH GALACTOSE
2j1e HIGH RESOLUTION CRYSTAL STRUCTURE OF CBM32 FROM A N-ACETYL-BETA-HEXOSAMINIDASE IN COMPLEX WITH LACNAC
2j62 STRUCTURE OF A BACTERIAL O-GLCNACASE IN COMPLEX WITH GLCNACSTATIN
2j7m CHARACTERIZATION OF A FAMILY 32 CBM