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(-) Description

Title :  CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANC, IN COMPLEX WITH 3-SIALYLLACTOSE
 
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 :  2.27
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 - PUTATIVE NEURAMINIDASE
    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: SIALIDASE NANC
    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  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1DAN2Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2SLT2Ligand/Ion5-(ACETYLAMINO)-3,5-DIDEOXYNON-2-ULOPYRANONOSYL-(2->3)-BETA-D-LYXO-HEXOPYRANOSYL-(1->4)HEXOPYRANOSE
3SO410Ligand/IonSULFATE ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2SLT1Ligand/Ion5-(ACETYLAMINO)-3,5-DIDEOXYNON-2-ULOPYRANONOSYL-(2->3)-BETA-D-LYXO-HEXOPYRANOSYL-(1->4)HEXOPYRANOSE
3SO45Ligand/IonSULFATE ION
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2SLT1Ligand/Ion5-(ACETYLAMINO)-3,5-DIDEOXYNON-2-ULOPYRANONOSYL-(2->3)-BETA-D-LYXO-HEXOPYRANOSYL-(1->4)HEXOPYRANOSE
3SO45Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:128 , PHE A:149 , ARG A:151 , GLU A:159 , ARG A:161 , ARG A:237 , PHE A:243 , HOH A:1150 , HOH A:1247binding site for residue SLT A 1001
02AC2SOFTWAREARG A:290 , ILE A:291 , ARG A:309 , ASP A:315 , ILE A:371 , ASP A:372 , ASP A:388 , PHE A:396 , TYR A:553 , SER A:582 , ARG A:600 , ARG A:662 , TYR A:695 , HOH A:1109 , HOH A:1110 , HOH A:1359binding site for residue DAN A 1002
03AC3SOFTWAREARG A:360 , ASN A:509 , SER A:514 , ASN A:719 , HOH A:1134binding site for residue SO4 A 1003
04AC4SOFTWARETYR A:181 , LYS A:182binding site for residue SO4 A 1004
05AC5SOFTWARETYR A:460 , HIS A:485 , ASN A:657 , HIS A:664 , HOH A:1136 , HOH A:1360 , HOH A:1364 , HOH A:1377binding site for residue SO4 A 1005
06AC6SOFTWAREASP A:422 , THR A:423 , ASP A:424 , ASN A:426 , HOH A:1209binding site for residue SO4 A 1006
07AC7SOFTWARETHR A:241 , ALA A:242 , PHE A:243 , GLY A:244 , HOH A:1293 , THR B:440 , ASN B:441 , ARG B:442binding site for residue SO4 A 1007
08AC8SOFTWARELEU B:128 , PHE B:149 , ARG B:151 , GLU B:159 , ARG B:161 , ARG B:237 , PHE B:243 , HOH B:901 , HOH B:988 , HOH B:999binding site for residue SLT B 801
09AC9SOFTWAREARG B:290 , ILE B:291 , ARG B:309 , ASP B:315 , ILE B:371 , ASP B:372 , ASP B:388 , PHE B:396 , TYR B:553 , SER B:582 , ARG B:600 , ARG B:662 , TYR B:695 , HOH B:1020 , HOH B:1057 , HOH B:1117 , HOH B:1176binding site for residue DAN B 802
10AD1SOFTWAREVAL B:357 , ARG B:360 , ASN B:509 , ASN B:719 , HOH B:1066binding site for residue SO4 B 803
11AD2SOFTWARETYR B:181 , LYS B:182 , HIS B:275 , HOH B:1132 , HOH B:1154binding site for residue SO4 B 804
12AD3SOFTWARETYR B:460 , HIS B:485 , HIS B:664 , SER B:689 , HOH B:1031 , HOH B:1120 , HOH B:1150binding site for residue SO4 B 805
13AD4SOFTWAREASP B:422 , THR B:423 , ASP B:424 , ASN B:426 , HOH B:1155binding site for residue SO4 B 806
14AD5SOFTWAREASN A:441 , ARG A:442 , HOH A:1259 , THR B:241 , PHE B:243 , HOH B:1182binding site for residue SO4 B 807

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YZ5)

(-) 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 4YZ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YZ5)

(-) Exons   (0, 0)

(no "Exon" information available for 4YZ5)

(-) 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: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..eeeeeeee..........eeeeeee.....eeeeeeee..........eeeee.....eeeee..................eeeehhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yz5 A  84 TPVLEKNNVTLTGGGENVTKELKDKFTSGDFTVVIKYNQSSEKGLQALFGISNSKPGQQNSYVDVFLRDNGELGMEARDTSSNKNNLVSRPASVWGKYKQEAVTNTVAVVADSVKKTYSLYANGTKVVEKKVDNFLNIKDIKGIDYYMLGGVKRAGKTAFGFNGTLENIKFFNSALDEETVKKMTTNAVTGHLIYTANDTTGSNYFRIPVLYTFSNGRVFSSIDARYGGTHDFLNKINIATSYSDDNGKTWTKPKLTLAFDDFAPVPLEWPREVGGRDLQISGGATYIDSVIVEKKNKQVLMFADVMPAGVSFREATRKDSGYKQIDGNYYLKLRKQGDTDYNYTIRENGTVYDDRTNRPTEFSVDKNFGIKQNGNYLTVEQYSVSFENKKTEYRNGTKVHMNIFYKDALFKVVPTNYIAYISSNDHGESWSAPTLLPPIMGLNRNAPYLGPGRGIIESSTGRILIPSYTGKESAFIYSDDNGASWKVKVVPLPSSWSAEAQFVELSPGVIQAYMRTNNGKIAYLTSKDAGTTWSAPEYLKFVSNPSYGTQLSIINYSQLIDGKKAVILSTPNSTNGRKHGQIWIGLINDDNTIDWRYHHDVDYSNYGYSYSTLTELPNHEIGLMFEKFDSWSRNELHMKNVVPYITFKIEDLKKN 740
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       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|                                                                                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                              473                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:654
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               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..............hhhhhh.......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..eeeeeeee..........eeeeeee.....eeeeeeee..........eeeee.....eeeee..................eeeehhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yz5 B  83 NTPVLEKNNVTLTGGGENVTKELKDKFTSGDFTVVIKYNQSSEKGLQALFGISNSKPGQQNSYVDVFLRDNGELGMEARDTSSNKNNLVSRPASVWGKYKQEAVTNTVAVVADSVKKTYSLYANGTKVVEKKVDNFLNIKDIKGIDYYMLGGVKRAGKTAFGFNGTLENIKFFNSALDEETVKKMTTNAVTGHLIYTANDTTGSNYFRIPVLYTFSNGRVFSSIDARYGGTHDFLNKINIATSYSDDNGKTWTKPKLTLAFDDFAPVPLEWPREVGGRDLQISGGATYIDSVIVEKKNKQVLMFADVMPAGVSFREATRKDSGYKQIDGNYYLKLRKQGDTDYNYTIRENGTVYDDRTNRPTEFSVDKNFGIKQNGNYLTVEQYSVSFKTEYRNGTKVHMNIFYKDALFKVVPTNYIAYISSNDHGESWSAPTLLPPIMGLNRNAPYLGPGRGIIESSTGRILIPSYTGKESAFIYSDDNGASWKVKVVPLPSSWSAEAQFVELSPGVIQAYMRTNNGKIAYLTSKDAGTTWSAPEYLKFVSNPSYGTQLSIINYSQLIDGKKAVILSTPNSTNGRKHGQIWIGLINDDNTIDWRYHHDVDYSNYGYSYSTLTELPNHEIGLMFEKFDSWSRNELHMKNVVPYITFKIEDLKKN 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       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736    
                                                                                                                                                                                                                                                                                                                                                                                                                             470|                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                              475
   Legend:   → Mismatch (orange background)
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  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 4YZ5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YZ5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YZ5)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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        A0A0H2UQE4_S | A0A0H2UQE4: 4yw1 4yw2 4yw3 4yw5 4yz1 4yz2 4yz3 4yz4

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