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(-) Description

Title :  THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES
 
Authors :  S. L. Newstead, J. A. Potter, J. C. Wilson, G. Xu, C. H. Chien, A. G. Watts, S. G. Withers, G. L. Taylor
Date :  17 Dec 07  (Deposition) - 22 Jan 08  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.97
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Sialidase, Glycosidase, Sialic Acid, Clostridium Perfringens (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
    Chains: A
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN, RESIDUES 243-694
    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  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:1551 , GLU A:1578 , TYR A:1631 , GLU A:1639 , HOH A:2225 , HOH A:2226 , HOH A:2227 , HOH A:2228 , HOH A:2797BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWAREGLU A:1578 , LYS A:1579 , ASP A:1580 , THR A:1581 , ASN A:1582 , GLU A:1639 , HOH A:2233 , HOH A:2235 , HOH A:2814BINDING SITE FOR RESIDUE GOL A 6
3AC3SOFTWAREASP A:1515 , TRP A:1573 , HOH A:2704 , HOH A:2708 , HOH A:2710 , HOH A:2713BINDING SITE FOR RESIDUE CA A 10
4AC4SOFTWAREASP A:1296 , ASP A:1298 , ASP A:1319 , TYR A:1320 , HOH A:2329 , HOH A:2330 , HOH A:2332 , HOH A:2384BINDING SITE FOR RESIDUE CA A 17

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VK5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:1292 -Pro A:1293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VK5)

(-) Exons   (0, 0)

(no "Exon" information available for 2VK5)

(-) 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 2vk5A01 A:1243-1360,A:1427-1691  [code=2.120.10.10, no name defined]                                                  ------------------------------------------------------------------2vk5A01 A:1243-1360,A:1427-1691  [code=2.120.10.10, no name defined]                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..hhhhh.eeeeeeeee.....eeeeeeee...........eeeeeeee..........eeee......eeeeeeeeee....eeeeeeeee..............eeee..eeeeeee.....eeeee..eee.....eeeeee....eeee..eeeee........ee....eeeeeee..........eehhhhhh......eee..ee.ee..hhhhh..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
                2vk5 A 1243 VEGAVKTEPVDLFHPGFLNSSNYRIPALFKTKEGTLIASIDARRHGGADAPNNDIDTAVRRSEDGGKTWDEGQIIMDYPDKSSVIDTTLIQDDETGRIFLLVTHFPSKYGFWNAGLGSGFKNIDGKEYLCLYDSSGKEFTVRENVVYDKDSNKTEYTTNALGDLFKNGTKIDNINSSTAPLKAKGTSYINLVYSDDDGKTWSEPQNINFQVKKDWMKFLGIAPGRGIQIKNGEHKGRIVVPVYYTNEKGKQSSAVIYSDDSGKNWTIGESPNDNRKLENGKIINSKTLSDDAPQLTECQVVEMPNGQLKLFMRNLSGYLNIATSFDGGATWDETVEKDTNVLEPYCQLSVINYSQKVDGKDAVIFSNPNARSRSNGTVRIGLINQVGTYENGEPKYEFDWKYNKLVKPGYYAYSCLTELSNGNIGLLYEGTPSEEMSYIEMNLKYLESG 1691
                                  1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402      1412      1422      1432      1442      1452      1462      1472      1482      1492      1502      1512      1522      1532      1542      1552      1562      1572      1582      1592      1602      1612      1622      1632      1642      1652      1662      1672      1682
   Legend:   → Mismatch (orange background)
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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 2VK5)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VK5)

(-) 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

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

UniProtKB/TrEMBL
        Q59310_CLOPF | Q59310: 2bf6 2vk6 2vk7

(-) Related Entries Specified in the PDB File

2bf6 ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA -SIALIC ACID (NEU5AC).
2vk6 THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES
2vk7 THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES