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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE

Authors :   G. Xu, J. A. Potter, R. J. M. Russell, M. R. Oggioni, P. W. Andrew, G. L. Taylor

Date :   13 Jun 08 (Deposition) - 24 Jun 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Sialidase, Glycosidase, Drug Design, Neuraminidase, Virulence Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Xu, J. A. Potter, R. J. M. Russell, M. R. Oggioni, P. W. Andrew, G. L. Taylor
Crystal Structure Of The Nanb Sialidase From Streptococcus Pneumoniae
J. Mol. Biol. V. 384 436 2008
PubMed-ID: 18835278 | Reference-DOI: 10.1016/J.JMB.2008.09.032

Molecule 1 - SIALIDASE B
	Chains	:	A
	EC Number	:	3.2.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Strain	:	TIGR
	Synonym	:	NANB SIALIDASE, NEURAMINIDASE B

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:253 , LYS A:315 , HOH A:2424	BINDING SITE FOR RESIDUE GOL A1697
2	AC2	SOFTWARE	TYR A:250 , THR A:251 , GLN A:494 , ILE A:596 , THR A:657 , HOH A:2425 , HOH A:2426	BINDING SITE FOR RESIDUE GOL A1698

(no "SS Bond" information available for 2VW0)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:271	-	Lys A:272

(no "SAP(SNP)/Variant" information available for 2VW0)

(no "PROSITE Motif" information available for 2VW0)

(no "Exon" information available for 2VW0)

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:657
 aligned with NANB_STRPN | Q54727 from UniProtKB/Swiss-Prot  Length:697

    Alignment length:657
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       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       
           NANB_STRPN    40 SPIFQGGSYQLNNKSIDISSLLLDKLSGESQTVVMKFKADKPNSLQALFGLSNSKAGFKNNYFSIFMRDSGEIGVEIRDAQKGINYLFSRPASLWGKHKGQAVENTLVFVSDSKDKTYTMYVNGIEVFSETVDTFLPISNINGIDKATLGAVNREGKEHYLAKGSIDEISLFNKAISDQEVSTIPLSNPFQLIFQSGDSTQANYFRIPTLYTLSSGRVLSSIDARYGGTHDSKSKINIATSYSDDNGKTWSEPIFAMKFNDYEEQLVYWPRDNKLKNSQISGSASFIDSSIVEDKKSGKTILLADVMPAGIGNNNANKADSGFKEINGHYYLKLKKNGDNDFRYTVRENGVVYNETTNKPTNYTINDKYEVLEGGKSLTVEQYSVDFDSGSLRERHNGKQVPMNVFYKDSLFKVTPTNYIAMTTSQNRGESWEQFKLLPPFLGEKHNGTYLCPGQGLALKSSNRLIFATYTSGELTYLISDDSGQTWKKSSASIPFKNATAEAQMVELRDGVIRTFFRTTTGKIAYMTSRDSGETWSKVSYIDGIQQTSYGTQVSAIKYSQLIDGKEAVILSTPNSRSGRKGGQLVVGLVNKEDDSIDWKYHYDIDLPSYGYAYSAITELPNHHIGVLFEKYDSWSRNELHLSNVVQYIDLEINDLT 696
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2vw0A02 A:229-357,A:456-696  [code=2.120.10.10, no name defined]                                                                 2vw0A03 A:358-455 Intramolecular Trans-sialidase; Domain 3                                        2vw0A02 A:229-357,A:456-696  [code=2.120.10.10, no name defined]                                                                                                                                                                                  CATH domains
               Pfam domains --Sialidase-2vw0A01 A:42-228                                                                                                                                                                 ---------------------------------------------------BNR-2vw0A02 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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...............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
                 2vw0 A  40 SPIFQGGSYQLNNKSIDISSLLLDKLSGESQTVVMKFKADKPNSLQALFGLSNSKAGFKNNYFSIFMRDSGEIGVEIRDAQKGINYLFSRPASLWGKHKGQAVENTLVFVSDSKDKTYTMYVNGIEVFSETVDTFLPISNINGIDKATLGAVNREGKEHYLAKGSIDEISLFNKAISDQEVSTIPLSNPFQLIFQSGDSTQANYFRIPTLYTLSSGRVLSSIDARYGGTHDSKSKINIATSYSDDNGKTWSEPIFAMKFNDYEEQLVYWPRDNKLKNSQISGSASFIDSSIVEDKKSGKTILLADVMPAGIGNNNANKADSGFKEINGHYYLKLKKNGDNDFRYTVRENGVVYNETTNKPTNYTINDKYEVLEGGKSLTVEQYSVDFDSGSLRERHNGKQVPMNVFYKDSLFKVTPTNYIAMTTSQNRGESWEQFKLLPPFLGEKHNGTYLCPGQGLALKSSNRLIFATYTSGELTYLISDDSGQTWKKSSASIPFKNATAEAQMVELRDGVIRTFFRTTTGKIAYMTSRDSGETWSKVSYIDGIQQTSYGTQVSAIKYSQLIDGKEAVILSTPNSRSGRKGGQLVVGLVNKEDDSIDWKYHYDIDLPSYGYAYSAITELPNHHIGVLFEKYDSWSRNELHLSNVVQYIDLEINDLT 696
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       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

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 '\|'

(no "SCOP Domain" information available for 2VW0)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Sialidase (8)

Streptococcus pneumoniae (3)

Sialidase-2vw0A01

A:42-228

Clan: Sialidase (56)

Family: BNR (5)

Streptococcus pneumoniae (3)

BNR-2vw0A02

A:280-291

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ser A:271 - Lys A:272	[ RasMol ]

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2vvz	STRUCTURE OF THE CATALYTIC DOMAIN OF STREPTOCOCCUS PNEUMONIAE SIALIDASE NANA
2vw1	CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE
2vw2	CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (0, 0)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (8, 8)

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