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(-) Description

Title :  CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANC, IN COMPLEX WITH N-ACETYLNEURAMINIC ACID.
 
Authors :  P. Lukacik, C. D. Owen, J. A. Potter, G. L. Taylor, M. A. Walsh
Date :  24 Mar 15  (Deposition) - 23 Sep 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sialidase, Neuraminidase, Beta-Propeller, Cbm40, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. D. Owen, P. Lukacik, J. A. Potter, O. Sleator, G. L. Taylor, M. A. Wals
Streptococcus Pneumoniae Nanc: Structural Insights Into The Specificity And Mechanism Of A Sialidase That Produces A Sialidase Inhibitor.
J. Biol. Chem. V. 290 27736 2015
PubMed-ID: 26370075  |  Reference-DOI: 10.1074/JBC.M115.673632

(-) Compounds

Molecule 1 - SIALIDASE, NANC
    Atcc: ATCC BAA-334
    Chains: A, B
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: POPINF
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 84-740
    Gene: SP_1326
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Strain: ATCC BAA-334 / TIGR4

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1SIA2Ligand/IonO-SIALIC ACID
2SO412Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1SIA1Ligand/IonO-SIALIC ACID
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1SIA1Ligand/IonO-SIALIC ACID
2SO46Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:128 , ASN A:143 , PHE A:149 , ARG A:151 , GLU A:159 , ARG A:161 , ARG A:237 , PHE A:243 , HOH A:1254binding site for residue SIA A 1001
02AC2SOFTWAREARG A:290 , ASP A:315 , ARG A:600 , ARG A:662 , TYR A:695 , TRP A:716binding site for residue SO4 A 1002
03AC3SOFTWAREVAL A:357 , ARG A:360 , ASN A:509 , SER A:514 , ASN A:719 , HOH A:1206binding site for residue SO4 A 1003
04AC4SOFTWARETYR A:181 , LYS A:182 , HOH A:1323binding site for residue SO4 A 1004
05AC5SOFTWARETYR A:460 , HIS A:485 , ASN A:657 , SER A:658 , HIS A:664 , HOH A:1230binding site for residue SO4 A 1005
06AC6SOFTWAREASP A:422 , THR A:423 , ASP A:424 , ASN A:426binding site for residue SO4 A 1006
07AC7SOFTWARETHR A:241 , ALA A:242 , PHE A:243 , HOH A:1229 , HOH A:1352 , ASN B:441binding site for residue SO4 A 1007
08AC8SOFTWARELEU B:128 , ASN B:143 , PHE B:149 , ARG B:151 , GLU B:159 , ARG B:161 , ARG B:237 , PHE B:243 , HOH B:1193 , HOH B:1254binding site for residue SIA B 1001
09AC9SOFTWAREARG B:290 , ASP B:315 , ARG B:600 , ARG B:662 , TYR B:695 , TRP B:716 , HOH B:1248 , HOH B:1282binding site for residue SO4 B 1002
10AD1SOFTWAREVAL B:357 , ARG B:360 , ASN B:509 , ASN B:719 , HOH B:1205binding site for residue SO4 B 1003
11AD2SOFTWARETYR B:181 , LYS B:182binding site for residue SO4 B 1004
12AD3SOFTWAREHIS B:485 , HIS B:664binding site for residue SO4 B 1005
13AD4SOFTWARETHR B:423 , ASP B:424 , ASN B:426binding site for residue SO4 B 1006
14AD5SOFTWARETHR A:440 , ASN A:441 , THR B:241 , PHE B:243 , GLY B:244 , HOH B:1310binding site for residue SO4 B 1007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YZ4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:316 -Leu A:317
2Phe B:316 -Leu B:317

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YZ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YZ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4YZ4)

(-) Sequences/Alignments

Asymmetric 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:655
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee...eehhhhhh.......eeeeeeeee......eeeeeee.........eeeeee.....eeeeeee....eeeeeee......ee..ee..eeeeeeee....eeeeee..eeeeeee..............eeee..eee..eee...eeeeeeeeee....hhhhhhhhhh..hhhhh...........eeeeeeeee.....eeeeeeee..........eeeeeeee..........eeee...........................eeeeeeeee.....eeeeeeee...............eeee..eeeeeeee.......eee....eeee....eeeeeee.....eee..ee.eeeeeeee...eeeeeeeeee.........ee.....eeeeeee..........ee............ee..ee.ee......eeeeee...eeeeeee.......eeeeee........eeeeeee..eeeeee.......eeeee..........ee.............eeeeeeeee..eeeeeeeee........eeeeeeee.....eeeeeeeee.........eeeee.....eeeee......hhhhh.......eeeehhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yz4 A  83 NTPVLEKNNVTLTGGGENVTKELKDKFTSGDFTVVIKYNQSSEKGLQALFGISNSKPGQQNSYVDVFLRDNGELGMEARDTSSNKNNLVSRPASVWGKYKQEAVTNTVAVVADSVKKTYSLYANGTKVVEKKVDNFLNIKDIKGIDYYMLGGVKRAGKTAFGFNGTLENIKFFNSALDEETVKKMTTNAVTGHLIYTANDTTGSNYFRIPVLYTFSNGRVFSSIDARYGGTHDFLNKINIATSYSDDNGKTWTKPKLTLAFDDFAPVPLEWPREVGGRDLQISGGATYIDSVIVEKKNKQVLMFADVMPAGVSFREATRKDSGYKQIDGNYYLKLRKQGDTDYNYTIRENGTVYDDRTNRPTEFSVDKNFGIKQNGNYLTVEQYSVSFEKTEYRNGTKVHMNIFYKDALFKVVPTNYIAYISSNDHGESWSAPTLLPPIMGLNRNAPYLGPGRGIIESSTGRILIPSYTGKESAFIYSDDNGASWKVKVVPLPSSWSAEAQFVELSPGVIQAYMRTNNGKIAYLTSKDAGTTWSAPEYLKFVSNPSYGTQLSIINYSQLIDGKKAVILSTPNSTNGRKHGQIWIGLINDDNTIDWRYHHDVDYSNYGYSYSTLTELPNHEIGLMFEKFDSWSRNELHMKNVVPYITFKIEDLKKN 740
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735     
                                                                                                                                                                                                                                                                                                                                                                                                                              471|                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                               475                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:656
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee...eehhhhhh.......eeeeeeeee......eeeeeee.........eeeeee.....eeeeeee....eeeeeee......ee..ee..eeeeeeee....eeeeee..eeeeeee..............eeee..eee..eee...eeeeeeeeee....hhhhhhhhhh..hhhhh...........eeeeeeeee.....eeeeeeee..........eeeeeeee..........eeee...........................eeeeeeeee.....eeeeeeee...............eeee..eeeeeeee.......eee....eeee....eeeeeee.....eee..ee.eeeeeeee....eeeeeeeeee.........ee.....eeeeeee..........ee............ee..ee.ee......eeeeee...eeeeeee.......eeeeee........eeeeeee..eeeeee.......eeeee..........ee.............eeeeeeeee..eeeeeeeee........eeeeeeee.....eeeeeeeee.........eeeee.....eeeee......hhhhh.......eeeehhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yz4 B  83 NTPVLEKNNVTLTGGGENVTKELKDKFTSGDFTVVIKYNQSSEKGLQALFGISNSKPGQQNSYVDVFLRDNGELGMEARDTSSNKNNLVSRPASVWGKYKQEAVTNTVAVVADSVKKTYSLYANGTKVVEKKVDNFLNIKDIKGIDYYMLGGVKRAGKTAFGFNGTLENIKFFNSALDEETVKKMTTNAVTGHLIYTANDTTGSNYFRIPVLYTFSNGRVFSSIDARYGGTHDFLNKINIATSYSDDNGKTWTKPKLTLAFDDFAPVPLEWPREVGGRDLQISGGATYIDSVIVEKKNKQVLMFADVMPAGVSFREATRKDSGYKQIDGNYYLKLRKQGDTDYNYTIRENGTVYDDRTNRPTEFSVDKNFGIKQNGNYLTVEQYSVSFEKKTEYRNGTKVHMNIFYKDALFKVVPTNYIAYISSNDHGESWSAPTLLPPIMGLNRNAPYLGPGRGIIESSTGRILIPSYTGKESAFIYSDDNGASWKVKVVPLPSSWSAEAQFVELSPGVIQAYMRTNNGKIAYLTSKDAGTTWSAPEYLKFVSNPSYGTQLSIINYSQLIDGKKAVILSTPNSTNGRKHGQIWIGLINDDNTIDWRYHHDVDYSNYGYSYSTLTELPNHEIGLMFEKFDSWSRNELHMKNVVPYITFKIEDLKKN 740
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734      
                                                                                                                                                                                                                                                                                                                                                                                                                              471|                                                                                                                                                                                                                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                               474
   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 4YZ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YZ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YZ4)

(-) Gene Ontology  (0, 0)

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    (no "Gene Ontology" information available for 4YZ4)

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UniProtKB/TrEMBL
        A0A0H2UQE4_S | A0A0H2UQE4: 4yw1 4yw2 4yw3 4yw5 4yz1 4yz2 4yz3 4yz5

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