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(-) Description

Title :  CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANB IN COMPLEX WITH 2,7-ANHYDRO-NEU5AC
 
Authors :  H. Gut, S. J. King, M. A. Walsh
Date :  26 Aug 08  (Deposition) - 16 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A
Keywords :  Intramolecular Trans-Sialidase, Lyase, Glycosidase, Neuraminidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Gut, S. J. King, M. A. Walsh
Structural And Functional Studies Of Streptococcus Pneumoniae Neuraminidase B: An Intramolecular Trans-Sialidase.
Febs Lett. V. 582 3348 2008
PubMed-ID: 18775704  |  Reference-DOI: 10.1016/J.FEBSLET.2008.08.026

(-) Compounds

Molecule 1 - SIALIDASE B
    Chains: A
    EC Number: 4.2.2.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 30-697
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4
    Synonym: NEURAMINIDASE B, NANB

 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
1EDO6Ligand/Ion1,2-ETHANEDIOL
2SKD1Ligand/Ion2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:245 , ILE A:246 , ARG A:264 , ASP A:270 , ILE A:326 , ASP A:327 , ASP A:344 , ASN A:352 , THR A:539 , GLU A:541 , ARG A:557 , ARG A:619 , TYR A:653 , TRP A:674 , HOH A:2457 , HOH A:3012 , HOH A:3013BINDING SITE FOR RESIDUE SKD A1698
2AC2SOFTWARELEU A:84 , SER A:103 , GLU A:115 , TYR A:199 , LYS A:335 , HOH A:3014 , HOH A:3015BINDING SITE FOR RESIDUE EDO A1699
3AC3SOFTWARETYR A:458 , ILE A:459 , LEU A:477 , PRO A:478 , PHE A:480 , HOH A:3016BINDING SITE FOR RESIDUE EDO A1700
4AC4SOFTWAREVAL A:385 , ILE A:404 , ASN A:405 , ASP A:406 , TYR A:408 , LYS A:475 , HOH A:2629 , HOH A:3017 , HOH A:3018 , HOH A:3019BINDING SITE FOR RESIDUE EDO A1701
5AC5SOFTWARETHR A:251 , GLN A:494 , ILE A:596 , THR A:657 , HOH A:2956 , HOH A:3020BINDING SITE FOR RESIDUE EDO A1702
6AC6SOFTWARESER A:617 , LYS A:620 , SER A:648 , HOH A:2911 , HOH A:3021 , HOH A:3022BINDING SITE FOR RESIDUE EDO A1703
7AC7SOFTWAREARG A:256 , ASN A:466 , ARG A:467 , GLU A:469 , SER A:617 , HOH A:2444 , HOH A:3023 , HOH A:3024BINDING SITE FOR RESIDUE EDO A1704

(-) SS Bonds  (0, 0)

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

(-) 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 2JKB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2JKB)

(-) 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:661
 aligned with NANB_STRPN | Q54727 from UniProtKB/Swiss-Prot  Length:697

    Alignment length:661
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696 
           NANB_STRPN    37 LSISPIFQGGSYQLNNKSIDISSLLLDKLSGESQTVVMKFKADKPNSLQALFGLSNSKAGFKNNYFSIFMRDSGEIGVEIRDAQKGINYLFSRPASLWGKHKGQAVENTLVFVSDSKDKTYTMYVNGIEVFSETVDTFLPISNINGIDKATLGAVNREGKEHYLAKGSIDEISLFNKAISDQEVSTIPLSNPFQLIFQSGDSTQANYFRIPTLYTLSSGRVLSSIDARYGGTHDSKSKINIATSYSDDNGKTWSEPIFAMKFNDYEEQLVYWPRDNKLKNSQISGSASFIDSSIVEDKKSGKTILLADVMPAGIGNNNANKADSGFKEINGHYYLKLKKNGDNDFRYTVRENGVVYNETTNKPTNYTINDKYEVLEGGKSLTVEQYSVDFDSGSLRERHNGKQVPMNVFYKDSLFKVTPTNYIAMTTSQNRGESWEQFKLLPPFLGEKHNGTYLCPGQGLALKSSNRLIFATYTSGELTYLISDDSGQTWKKSSASIPFKNATAEAQMVELRDGVIRTFFRTTTGKIAYMTSRDSGETWSKVSYIDGIQQTSYGTQVSAIKYSQLIDGKEAVILSTPNSRSGRKGGQLVVGLVNKEDDSIDWKYHYDIDLPSYGYAYSAITELPNHHIGVLFEKYDSWSRNELHLSNVVQYIDLEINDLTK 697
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2jkbA02 A:229-357,A:456-697  [code=2.120.10.10, no name defined]                                                                 2jkbA03 A:358-455 Intramolecular Trans-sialidase; Domain 3                                        2jkbA02 A:229-357,A:456-697  [code=2.120.10.10, no name defined]                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee...eehhhhhhhhh....eeeeeeee......eeeeeeee.........eeeeeee....eeeeeee....eeeeeee......ee..ee..eeeeeeee....eeeeee..eeeeeee.....hhhhh....eeee..eee..eee...eeeeeeeeee....hhhhhhh....................eee....ee.....eeeeeeee..........eeeeeeee..........eeee...........................eeeeeeeee......eeeeeeee...............eee....eeeeeee.......eee....eeee....eeeeeee.....eee..ee.eeeeeeee......eeeeeeeeee.........ee.....eeeeeee..........ee............ee..ee.ee......eeeeeee..eeeeeee.......eeeeee.........eeeeeee..eeeeee.......eeeee..........ee.............eeeeeeeee..eeeeeeeee........eeeeeeee......eeeeeeee..........eeeee.....eeeeee...............eeeeeehhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jkb A  37 LSISPIFQGGSYQLNNKSIDISSLLLDKLSGESQTVVMKFKADKPNSLQALFGLSNSKAGFKNNYFSIFMRDSGEIGVEIRDAQKGINYLFSRPASLWGKHKGQAVENTLVFVSDSKDKTYTMYVNGIEVFSETVDTFLPISNINGIDKATLGAVNREGKEHYLAKGSIDEISLFNKAISDQEVSTIPLSNPFQLIFQSGDSTQANYFRIPTLYTLSSGRVLSSIDARYGGTHDSKSKINIATSYSDDNGKTWSEPIFAMKFNDYEEQLVYWPRDNKLKNSQISGSASFIDSSIVEDKKSGKTILLADVMPAGIGNNNANKADSGFKEINGHYYLKLKKNGDNDFRYTVRENGVVYNETTNKPTNYTINDKYEVLEGGKSLTVEQYSVDFDSGSLRERHNGKQVPMNVFYKDSLFKVTPTNYIAMTTSQNRGESWEQFKLLPPFLGEKHNGTYLCPGQGLALKSSNRLIFATYTSGELTYLISDDSGQTWKKSSASIPFKNATAEAQMVELRDGVIRTFFRTTTGKIAYMTSRDSGETWSKVSYIDGIQQTSYGTQVSAIKYSQLIDGKEAVILSTPNSRSGRKGGQLVVGLVNKEDDSIDWKYHYDIDLPSYGYAYSAITELPNHHIGVLFEKYDSWSRNELHLSNVVQYIDLEINDLTK 697
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696
   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 2JKB)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NANB_STRPN | Q54727)
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: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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    Ser A:271 - Lys A:272   [ RasMol ]  
 

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  NANB_STRPN | Q54727
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 Related Entries

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

UniProtKB/Swiss-Prot
        NANB_STRPN | Q54727: 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 4xmi 4xog 4xyx

(-) Related Entries Specified in the PDB File

2vw0 CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE
2vw1 CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE
2vw2 CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE