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(-) Description

Title :  SIALIDASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH APANA AND EPANA INHIBITORS
 
Authors :  E. F. Garman, S. C. Crennell, E. R. Vimr, W. G. Laver, G. L. Taylor
Date :  23 Apr 96  (Deposition) - 07 Dec 96  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Crennell, E. F. Garman, C. Philippon, A. Vasella, W. G. Laver, E. R. Vimr, G. L. Taylor
The Structures Of Salmonella Typhimurium Lt2 Neuraminidase And Its Complexes With Three Inhibitors At High Resolution.
J. Mol. Biol. V. 259 264 1996
PubMed-ID: 8656428  |  Reference-DOI: 10.1006/JMBI.1996.0318
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIALIDASE
    Chains: A
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: NANH
    Expression System Plasmid: PSX62
    Expression System Taxid: 562
    Expression System Vector Type: BACTERIAL
    Gene: NANH
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Other Details: RESIDUE MET 1 WAS EXCISED BY ESCHERICHIA COLI
    Strain: LT2
    Variant: TA263, PROTOTROPH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1AXP1Ligand/Ion4-ACETAMIDO-2,4-DIDEXOY-D-GLYCERO-BETA-D-GALACTO-OCTOPYRANOSYLPHOSPHONIC ACID (AN AXIAL PHOSPHONATE)
2EQP1Ligand/Ion(4-ACETAMIDO-2,4-DIDEOXY-D-GLYCERO-ALPHA-D-GALACTO-1-OCTOPYRANOSYL)PHOSPHONIC ACID
3K1Ligand/IonPOTASSIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:37 , ARG A:56 , ASP A:62 , MET A:99 , ASP A:100 , THR A:127 , TRP A:128 , ARG A:246 , ARG A:309 , TYR A:342 , AXP A:384 , HOH A:664 , HOH A:688 , HOH A:689 , K A:690 , HOH A:691 , HOH A:692 , HOH A:693 , HOH A:694 , HOH A:695 , HOH A:696BINDING SITE FOR RESIDUE EQP A 383
2AC2SOFTWAREARG A:37 , ARG A:56 , ASP A:62 , MET A:99 , ASP A:100 , THR A:127 , TRP A:128 , ARG A:246 , ARG A:309 , TYR A:342 , EQP A:383 , HOH A:688 , HOH A:689 , K A:690 , HOH A:692 , HOH A:693 , HOH A:694 , HOH A:695 , HOH A:696BINDING SITE FOR RESIDUE AXP A 384
3AC3SOFTWAREASP A:62 , EQP A:383 , AXP A:384 , HOH A:697BINDING SITE FOR RESIDUE K A 690
4ACTUNKNOWNARG A:37 , ARG A:56 , ASP A:62 , MET A:99 , ASP A:100 , TRP A:121 , TRP A:128 , LEU A:175 , GLU A:231 , ARG A:246 , ARG A:309 , TYR A:342 , GLU A:361ACTIVE SITE

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:103

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:135 -Pro A:136

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DIL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DIL)

(-) Exons   (0, 0)

(no "Exon" information available for 1DIL)

(-) 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:381
 aligned with NANH_SALTY | P29768 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:381
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381 
           NANH_SALTY     2 TVEKSVVFKAEGEHFTDQKGNTIVGSGSGGTTKYFRIPAMCTTSKGTIVVFADARHNTASDQSFIDTAAARSTDGGKTWNKKIAIYNDRVNSKLSRVMDPTCIVANIQGRETILVMVGKWNNNDKTWGAYRDKAPDTDWDLVLYKSTDDGVTFSKVETNIHDIVTKNGTISAMLGGVGSGLQLNDGKLVFPVQMVRTKNITTVLNTSFIYSTDGITWSLPSGYCEGFGSENNIIEFNASLVNNIRNSGLRRSFETKDFGKTWTEFPPMDKKVDNRNHGVQGSTITIPSGNKLVAAHSSAQNKNNDYTRSDISLYAHNLYSGEVKLIDDFYPKVGNASGAGYSCLSYRKNVDKETLYVVYEANGSIEFQDLSRHLPVIKSYN 382
               SCOP domains d1dila_ A: Salmonella sialidase                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1dilA00 A:2-382  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........................eee..eeee.....eeeeeeee.........eeeeeeee.......eeeeee..........eee..eeeeeee..eeeeeeeeeee......hhh..........eeeeeee.............hhhhhhhh..eeeeee............eeeeeeeee.......eeeeeeee...................eeeeee..eeeeee......eeeee..........................eeeeeee..eeeeeeeee...........eeeeee......eeeee..............eeeeeeee..eeeeeeeeee..eeeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dil A   2 TVEKSVVFKAEGEHFTDQKGNTIVGSGSGGTTKYFRIPAMCTTSKGTIVVFADARHNTASDQSFIDTAAARSTDGGKTWNKKIAIYNDRVNSKLSRVMDPTCIVANIQGRETILVMVGKWNNNDKTWGAYRDKAPDTDWDLVLYKSTDDGVTFSKVETNIHDIVTKNGTISAMLGGVGSGLQLNDGKLVFPVQMVRTKNITTVLNTSFIYSTDGITWSLPSGYCEGFGSENNIIEFNASLVNNIRNSGLRRSFETKDFGKTWTEFPPMDKKVDNRNHGVQGSTITIPSGNKLVAAHSSAQNKNNDYTRSDISLYAHNLYSGEVKLIDDFYPKVGNASGAGYSCLSYRKNVDKETLYVVYEANGSIEFQDLSRHLPVIKSYN 382
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DIL)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NANH_SALTY | P29768)
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.
biological process
    GO:0006689    ganglioside catabolic process    The chemical reactions and pathways resulting in the breakdown of ganglioside, a ceramide oligosaccharide carrying, in addition to other sugar residues, one or more sialic residues.
    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:0009313    oligosaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NANH_SALTY | P29768: 1dim 2sil 2sim 3sil

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