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(-) Description

Title :  CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE D39 NEURAMINIDASE A PRECURSOR (NANA) IN COMPLEX WITH DANA
 
Authors :  Y. -S. Hsiao, L. Tong
Date :  24 Apr 09  (Deposition) - 12 May 09  (Release) - 12 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Six-Bladed Beta-Propeller, Cell Wall, Glycosidase, Hydrolase, Peptidoglycan-Anchor, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. -S. Hsiao, D. Parker, A. J. Ratner, A. Prince, L. Tong
Crystal Structures Of Respiratory Pathogen Neuraminidases
Biochem. Biophys. Res. Commun. V. 380 467 2009
PubMed-ID: 19284989  |  Reference-DOI: 10.1016/J.BBRC.2009.01.108
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIALIDASE A
    Chains: A, B
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PET28A
    Fragment: UNP RESIDUES 317-793
    Gene: NANA, SPR1536
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6
    Synonym: NEURAMINIDASE A

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1DAN2Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:27 , HOH A:52 , ARG A:347 , ILE A:348 , ARG A:366 , ASP A:372 , ILE A:416 , ASP A:417 , ASP A:434 , ILE A:442 , PHE A:443 , TYR A:590 , GLN A:602 , ARG A:663 , ARG A:721 , TYR A:752 , HOH A:995 , HOH A:1066BINDING SITE FOR RESIDUE DAN A 900
2AC2SOFTWAREHOH B:45 , HOH B:79 , HOH B:188 , ARG B:347 , ILE B:348 , ARG B:366 , ASP B:372 , ILE B:416 , ASP B:417 , ASP B:434 , ILE B:442 , PHE B:443 , TYR B:590 , GLN B:602 , ARG B:663 , ARG B:721 , TYR B:752 , HOH B:1027 , HOH B:1062BINDING SITE FOR RESIDUE DAN B 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H73)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:718 -Pro A:719
2Ala A:776 -Tyr A:777
3Gly B:718 -Pro B:719
4Ala B:776 -Tyr B:777

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H73)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H73)

(-) Exons   (0, 0)

(no "Exon" information available for 3H73)

(-) 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:474
 aligned with NANA_STRR6 | P62576 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:474
                                   329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789    
           NANA_STRR6   320 GAALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSKDL 793
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeee..............eeeeeeeee.....eeeeeeee.........eeeeeeee..........eeee.........hhhhh..eeeeeeeee......eeeeeeee...hhhhhh.......eee....eeeee........eee....eee.....eeeeee.....hhhhh...eeee..eeeee.................eeeeeee..........eehhhhhh......eee..ee.ee.........eeeeeee....hhhhhh.eeeeeee.......ee.......eee..eee......hhhhh...eeeee.....eeeee.....eeeeeee...........eeeeeee......eeeeeee..eeeeeeeee.....eeeeeeeeee.....eeeeeeeeeeeee...eeeeeee..eeeeeeee........eeeeeeeehhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3h73 A 320 GAALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSKDL 793
                                   329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789    


Chain B from PDB  Type:PROTEIN  Length:477
 aligned with NANA_STRR6 | P62576 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:477
                                   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       706       716       726       736       746       756       766       776       786       
           NANA_STRR6   317 LPEGAALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSKDL 793
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee..............eeeeeeeee.....eeeeeeee.........eeeeeeee..........eeee.........hhhhh..eeeeeeeee......eeeeeeee...hhhhhh.......eeee..eeeeeeee......eee....eee.....eeeeee.....hhhhh...eeee..eeeee..........ee.....eeeeeee..........eehhhhhh......eee..ee.ee.........eeeeeee....hhhhhh.eeeeeee.......ee........ee..ee...............eeeee.....eeeee.....eeeeeee...........eeeeeee......eeeeeee..eeeeeeeee.....eeeeeeeeee.....eeeeeeeeeeeee...eeeeeee..eeeeeeee........eeeeeeeehhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h73 B 317 LPEGAALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSKDL 793
                                   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       706       716       726       736       746       756       766       776       786
   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 3H73)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H73)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H73)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NANA_STRR6 | P62576)
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: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.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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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    Ala A:776 - Tyr A:777   [ RasMol ]  
    Ala B:776 - Tyr B:777   [ RasMol ]  
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  3h73
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  NANA_STRR6 | P62576
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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
        NANA_STRR6 | P62576: 2w20 3h71 3h72

(-) Related Entries Specified in the PDB File

3h6j CRYSTAL STRUCTURE OF A PUTATIVE NEURAMINIDASE FROM PSEUDOMONAS AERUGINOSA
3h71 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE D39 NEURAMINIDASE A PRECURSOR (NANA), FREE ENZYME
3h72 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE D39 NEURAMINIDASE A PRECURSOR (NANA) IN COMPLEX WITH NANA