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(-) Description

Title :  CRYSTAL STRUCTURE OF THE K499G MUTANT OF NANB SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  P. Brear
Date :  14 Jan 15  (Deposition) - 13 Jan 16  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Intramolecular Trans-Sialidase, Glycosidase, Drug Design, Neuraminidase, Allosteric Inhibitor, Serendipitous Allosteric Sites, Crystallization Artefacts (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. W. Rogers, P. Brear, L. Yang, A. S. Chen, J. B. O. Mitchell, G. L. Taylor, N. J. Westwood
The Hunt For Serendipitous Allosteric Sites: Discovery Of A Novel Allosteric Inhibitor Of The Bacterial Sialidase Nanb
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SIALIDASE B
    Chains: A
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET23B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 39-696
    Gene: NANB, SP_1687
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE SEROTYPE 4 (STRAIN ATCC BAA-334 / TIGR4)
    Organism Taxid: 170187
    Synonym: NEURAMINIDASE B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1DMS6Ligand/IonDIMETHYL SULFOXIDE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:105 , ARG A:107 , GLU A:115binding site for residue DMS A 701
2AC2SOFTWAREARG A:129 , GLU A:165 , VAL A:166 , SER A:682 , HOH A:1453 , HOH A:1508binding site for residue DMS A 702
3AC3SOFTWARETYR A:160 , GLY A:163 , ASP A:217 , VAL A:220 , HOH A:1148 , HOH A:1209binding site for residue DMS A 703
4AC4SOFTWAREARG A:245 , ILE A:246 , ARG A:264 , ASP A:270 , ILE A:326 , ASP A:327 , GLU A:541 , TYR A:653binding site for residue PO4 A 704
5AC5SOFTWARETYR A:250 , THR A:251 , GLN A:494 , THR A:657 , HOH A:1238binding site for residue DMS A 705
6AC6SOFTWAREGLU A:194 , ASP A:448 , LEU A:450 , HOH A:814binding site for residue DMS A 706
7AC7SOFTWAREPHE A:294 , ALA A:295 , MET A:296 , LYS A:297 , TRP A:471binding site for residue DMS A 707

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:271 -Lys A:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XMI)

(-) 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:658
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee...eehhhhhhhhh....eeeeeeee......eeeeeeee.........eeeeeee....eeeeeee....eeeeeee......ee..ee..eeeeeeee....eeeeee..eeeeeee..............eeee..eee..eee...eeeeeeeeee....hhhhhh.....................eee....ee.....eeeeeeee..........eeeeeeee..........eeee...........................eeeeeeeee......eeeeeeee....hhhhh......eeee..eeeeeeee.......eee....eeee....eeeeeee.....eee..ee.eeeeeeee......eeeeeeeeee.........ee.....eeeeeee..........ee............ee..ee.ee......eeeeeee..eeeeeee.......eeeeee.........eeeeeee..eeeeee.......eeeee..........ee.............eeee.........eeeeeee........eeeeeeee......eeeeeeee..........eeeee.....eeeeee...............eeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xmi A  39 ISPIFQGGSYQLNNKSIDISSLLLDKLSGESQTVVMKFKADKPNSLQALFGLSNSKAGFKNNYFSIFMRDSGEIGVEIRDAQKGINYLFSRPASLWGKHKGQAVENTLVFVSDSKDKTYTMYVNGIEVFSETVDTFLPISNINGIDKATLGAVNREGKEHYLAKGSIDEISLFNKAISDQEVSTIPLSNPFQLIFQSGDSTQANYFRIPTLYTLSSGRVLSSIDARYGGTHDSKSKINIATSYSDDNGKTWSEPIFAMKFNDYEEQLVYWPRDNKLKNSQISGSASFIDSSIVEDKKSGKTILLADVMPAGIGNNNANKADSGFKEINGHYYLKLKKNGDNDFRYTVRENGVVYNETTNKPTNYTINDKYEVLEGGKSLTVEQYSVDFDSGSLRERHNGKQVPMNVFYKDSLFKVTPTNYIAMTTSQNRGESWEQFKLLPPFLGEKHNGTYLCPGQGLALGSSNRLIFATYTSGELTYLISDDSGQTWKKSSASIPFKNATAEAQMVELRDGVIRTFFRTTTGKIAYMTSRDSGETWSKVSYIDGIQQTSYGTQVSAIKYSQLIDGKEAVILSTPNSRSGRKGGQLVVGLVNKEDDSIDWKYHYGIDLPSYGYAYSAITELPNHHIGVLFEKYDSWSRNELHLSNVVQYIDLEINDLT 696
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688
   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 4XMI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ser A:271 - Lys A:272   [ RasMol ]  
 

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  NANB_STRPN | Q54727
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  3.2.1.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        NANB_STRPN | Q54727: 2jkb 2vw0 2vw1 2vw2 4foq 4fov 4fow 4foy 4fp2 4fp3 4fpc 4fpe 4fpf 4fpg 4fph 4fpj 4fpk 4fpl 4fpo 4fpy 4fq4 4xe9 4xhb 4xhx 4xik 4xil 4xio 4xj8 4xj9 4xja 4xju 4xjw 4xjz 4xma 4xog 4xyx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4XMI)