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(-) Description

Title :  ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA-SIALIC ACID (NEU5AC).
 
Authors :  S. Newstead, G. L. Taylor
Date :  04 Dec 04  (Deposition) - 09 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.97
Chains :  Asym./Biol. Unit :  A
Keywords :  Sialidase, Clostridium Perfringens, Sialic Acid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. L. Newstead, J. A. Potter, J. C. Wilson, G. Xu, C. H. Chien, A. G. Watts, S. G. Withers, G. L. Taylor
The Structure Of Clostridium Perfringens Nani Sialidase And Its Catalytic Intermediates.
J. Biol. Chem. V. 283 9080 2008
PubMed-ID: 18218621  |  Reference-DOI: 10.1074/JBC.M710247200

(-) Compounds

Molecule 1 - EXO-ALPHA-SIALIDASE
    Atcc: 10543
    Chains: A
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector: PMAL-C2
    Fragment: RESIDUES 243-691
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502
    Synonym: SIALIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:266 , ILE A:267 , ARG A:285 , ASP A:291 , ILE A:327 , ASP A:328 , PHE A:353 , TYR A:485 , GLN A:493 , ARG A:555 , TYR A:587 , ARG A:615 , TYR A:655 , HOH A:2032 , HOH A:2337 , HOH A:2481BINDING SITE FOR RESIDUE SIA A1692
2AC2SOFTWAREASP A:296 , ASP A:298 , ASP A:319 , TYR A:320 , HOH A:2039 , HOH A:2042 , HOH A:2071BINDING SITE FOR RESIDUE CA A1693
3AC3SOFTWAREASP A:515 , TRP A:573 , HOH A:2193 , HOH A:2303 , HOH A:2306 , HOH A:2309BINDING SITE FOR RESIDUE CA A1694
4AC4SOFTWARELYS A:551 , GLU A:578 , TYR A:631 , GLU A:639 , HOH A:2353 , HOH A:2482 , HOH A:2483 , HOH A:2484BINDING SITE FOR RESIDUE GOL A1695
5AC5SOFTWAREGLU A:578 , LYS A:579 , ASP A:580 , THR A:581 , ASN A:582 , GLU A:639 , HOH A:2431 , HOH A:2485BINDING SITE FOR RESIDUE GOL A1696

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BF6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:292 -Pro A:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BF6)

(-) Exons   (0, 0)

(no "Exon" information available for 2BF6)

(-) 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:449
 aligned with Q59310_CLOPF | Q59310 from UniProtKB/TrEMBL  Length:694

    Alignment length:449
                                   252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682         
         Q59310_CLOPF   243 VEGAVKTEPVDLFHPGFLNSSNYRIPALFKTKEGTLIASIDARRHGGADAPNNDIDTAVRRSEDGGKTWDEGQIIMDYPDKSSVIDTTLIQDDETGRIFLLVTHFPSKYGFWNAGLGSGFKNIDGKEYLCLYDSSGKEFTVRENVVYDKDGNKTEYTTNALGDLFKNGTKIDNINSSTAPLKAKGTSYINLVYSDDDGKTWSEPQNINFQVKKDWMKFLGIAPGRGIQIKNGEHKGRIVVPVYYTNEKGKQSSAVIYSDDSGKNWTIGESPNDNRKLENGKIINSKTLSDDAPQLTECQVVEMPNGQLKLFMRNLSGYLNIATSFDGGATWDETVEKDTNVLEPYCQLSVINYSQKVDGKDAVIFSNPNARSRSNGTVRIGLINQVGTYENGEPKYEFDWKYNKLVKPGYYAYSCLTELSNGNIGLLYEGTPSEEMSYIEMNLKYLESG 691
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2bf6A01 A:243-360,A:427-691  [code=2.120.10.10, no name defined]                                                      ------------------------------------------------------------------2bf6A01 A:243-360,A:427-691  [code=2.120.10.10, no name defined]                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..hhhhh.eeeeeeeee.....eeeeeeee...........eeeeeeee..........eeee......eeeeeeeee......eeeeeeee..............eeee..eeeeeee.....eeeee..eee.....eeeeee....eeee..eeeee........ee....eeeeeee..........eehhhhhh......eee..ee.ee.........eeeeeeee.....eeeeeeee.......ee.......ee.....ee...........eeeeeeee.....eeeeeee...eeeeeee...........eeeeeee......eeee.........eeeeeee.....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee...eeeee.....eeeee.......eeeeeehhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bf6 A 243 VEGAVKTEPVDLFHPGFLNSSNYRIPALFKTKEGTLIASIDARRHGGADAPNNDIDTAVRRSEDGGKTWDEGQIIMDYPDKSSVIDTTLIQDDETGRIFLLVTHFPSKYGFWNAGLGSGFKNIDGKEYLCLYDSSGKEFTVRENVVYDKDSNKTEYTTNALGDLFKNGTKIDNINSSTAPLKAKGTSYINLVYSDDDGKTWSEPQNINFQVKKDWMKFLGIAPGRGIQIKNGEHKGRIVVPVYYTNEKGKQSSAVIYSDDSGKNWTIGESPNDNRKLENGKIINSKTLSDDAPQLTECQVVEMPNGQLKLFMRNLSGYLNIATSFDGGATWDETVEKDTNVLEPYCQLSVINYSQKVDGKDAVIFSNPNARSRSNGTVRIGLINQVGTYENGEPKYEFDWKYNKLVKPGYYAYSCLTELSNGNIGLLYEGTPSEEMSYIEMNLKYLESG 691
                                   252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682
   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 2BF6)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BF6)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q59310_CLOPF | Q59310)
molecular function
    GO:0052794    exo-alpha-(2->3)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052795    exo-alpha-(2->6)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052796    exo-alpha-(2->8)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
    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: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.
    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.
    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.

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  3.2.1.18
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 Related Entries

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UniProtKB/TrEMBL
        Q59310_CLOPF | Q59310: 2vk5 2vk6 2vk7

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