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(-) Description

Title :  THE STRUCTURE OF THE FAMILY 32 CBM FROM C. PERFRINGENS NANJ IN COMPLEX WITH GALACTOSE
 
Authors :  A. B. Boraston, E. Ficko-Blean, M. Healey
Date :  25 Jul 07  (Deposition) - 21 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Galactose, Bacterial Pathogen, Carbohydrate-Binding Module, Sugar-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Boraston, E. Ficko-Blean, M. Healey
Carbohydrate Recognition By A Large Sialidase Toxin From Clostridium Perfringens.
Biochemistry V. 46 11352 2007
PubMed-ID: 17850114  |  Reference-DOI: 10.1021/BI701317G

(-) Compounds

Molecule 1 - EXO-ALPHA-SIALIDASE
    Atcc: 13124
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 42-180
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502
    Synonym: CBM32

 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
1CA1Ligand/IonCALCIUM ION
2GAL1Ligand/IonBETA-D-GALACTOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:26 , ASP A:29 , ASN A:31 , THR A:34 , ALA A:132 , GLU A:133BINDING SITE FOR RESIDUE CA A1139
2AC2SOFTWAREHIS A:37 , TRP A:40 , ARG A:68 , ASN A:73 , HOH A:2042BINDING SITE FOR RESIDUE GAL A1140

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V72)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:46 -Pro A:47
2Asn A:86 -Gly A:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V72)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V72)

(-) Exons   (0, 0)

(no "Exon" information available for 2V72)

(-) 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:137
 aligned with Q8XMY5_CLOPE | Q8XMY5 from UniProtKB/TrEMBL  Length:1173

    Alignment length:137
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       
         Q8XMY5_CLOPE    44 IETAIPQSEMTASATSEEGQDPASSAIDGNINTMWHTKWNGSDALPQSLSVNLGKARKVSSIAITPRTSGNNGFITKYEIHAINNGVETLVAEGTWEENNLVKTVTFDSPIDAEEIKITAIQGVGGFASIAELNVYE 180
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----F5_F8_type_C-2v72A02 A:6-134                                                                                                     Sial Pfam domains
         Sec.struct. author .....hhhhheeee.......hhhhhh.......ee..........eeeeeeeeeeeeeeeeeee.........eeeeeeeeee..eeeeeeeee.......eeeeeeeeeeeeeeeeeeeee.hhh.ee.eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v72 A   2 IETAIPQSEMTASATSEEGQDPASSAIDGNINTMWHTKWNGSDALPQSLSVNLGKARKVSSIAITPRTSGNNGFITKYEIHAINNGVETLVAEGTWEENNLVKTVTFDSPIDAEEIKITAIQGVGGFASIAELNVYE 138
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 2V72)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V72)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Concanavalin (293)
(-)
Clan: GBD (153)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8XMY5_CLOPE | Q8XMY5)
molecular function
    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:0004308    exo-alpha-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

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(-) Related Entries Specified in the PDB File

2v73 THE STRUCTURE OF THE FAMILY 40 CBM FROM C. PERFRINGENS NANJ IN COMPLEX WITH A SIALIC ACID CONTAINING MOLECULE