2W20 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE CATALYTIC DOMAIN OF THE NATIVE NANA SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE

Authors :   G. Xu, P. W. Andrew, G. L. Taylor

Date :   21 Oct 08 (Deposition) - 23 Dec 08 (Release) - 10 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.49

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Secreted, Cell Wall, Hydrolase, Sialidase, Glycosidase, Neuraminidase, Peptidoglycan-Anchor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Xu, X. Li, P. W. Andrew, G. L. Taylor
Structure Of The Catalytic Domain Of Streptococcus Pneumoniae Sialidase Nana.
Acta Crystallogr. , Sect. F V. 64 772 2008
PubMed-ID: 18765901 | Reference-DOI: 10.1107/S1744309108024044

Molecule 1 - SIALIDASE A
	Chains	:	A, B
	EC Number	:	3.2.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 321-791
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	171101
	Strain	:	R6
	Synonym	:	NEURAMINIDASE A, NANA SIALIDASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:465 , ARG A:466 , GLU A:467 , GLY A:468 , GLU A:469 , ARG A:529 , HOH A:2559 , HOH A:2560 , ASN B:625 , LYS B:632	BINDING SITE FOR RESIDUE MES A1791
2	AC2	SOFTWARE	ASN A:625 , LYS A:632 , GLU B:450 , TYR B:465 , ARG B:466 , GLU B:467 , GLY B:468 , GLU B:469 , LYS B:470 , ARG B:529 , GOL B:1793 , HOH B:2465	BINDING SITE FOR RESIDUE MES B1791
3	AC3	SOFTWARE	ASN B:517 , LYS B:524 , THR B:525 , SER B:526	BINDING SITE FOR RESIDUE CL B1792
4	AC4	SOFTWARE	GLY A:516 , ASN A:517 , LYS A:524 , THR A:525 , SER A:526	BINDING SITE FOR RESIDUE CL A1792
5	AC5	SOFTWARE	VAL A:628 , GLN A:631 , HOH A:2396 , HOH A:2403	BINDING SITE FOR RESIDUE CL A1793
6	AC6	SOFTWARE	GLN A:627 , LYS A:632 , LYS A:683 , GLU B:469 , LYS B:470 , MES B:1791	BINDING SITE FOR RESIDUE GOL B1793
7	AC7	SOFTWARE	ASP A:385 , ASN A:386 , GLU A:762 , LYS A:783 , HOH A:2057 , ASP B:490 , LYS B:510	BINDING SITE FOR RESIDUE GOL A1794
8	AC8	SOFTWARE	SER A:371 , TRP A:373 , SER A:409 , ILE A:410 , GLU A:425 , HIS A:612	BINDING SITE FOR RESIDUE GOL A1795

(no "SS Bond" information available for 2W20)

Asymmetric Unit

No.	Residues
1	Gly A:718	-	Pro A:719
2	Asn A:734	-	Gly A:735
3	Ala A:776	-	Tyr A:777
4	Gly B:718	-	Pro B:719
5	Ala B:776	-	Tyr B:777

(no "SAP(SNP)/Variant" information available for 2W20)

(no "PROSITE Motif" information available for 2W20)

(no "Exon" information available for 2W20)

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:470
 aligned with NANA_STRR6 | P62576 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:470
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790
           NANA_STRR6   321 AALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLS 790
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w20A01 A:321-451,A:532-790  [code=2.120.10.10, no name defined]                                                                   --------------------------------------------------------------------------------2w20A01 A:321-451,A:532-790  [code=2.120.10.10, no name defined]                                                                                                                                                                                                    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.......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
                 2w20 A 321 AALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLS 790
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790

Chain B from PDB  Type:PROTEIN  Length:469
 aligned with NANA_STRR6 | P62576 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:469
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781         
           NANA_STRR6   322 ALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLS 790
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w20B01 B:322-451,B:532-790  [code=2.120.10.10, no name defined]                                                                  --------------------------------------------------------------------------------2w20B01 B:322-451,B:532-790  [code=2.120.10.10, no name defined]                                                                                                                                                                                                    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.......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
                 2w20 B 322 ALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLS 790
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781

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 2W20)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 6 Propellor (215)

Topology: Neuraminidase (215)

Homologous Superfamily: [code=2.120.10.10, no name defined] (150)

Streptococcus pneumoniae. Organism_taxid: 171101. Strain: r6. (1)

1a	2w20B01	B:322-451,B:532-790
1b	2w20A01	A:321-451,A:532-790

(no "Pfam Domain" information available for 2W20)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:776 - Tyr A:777	[ RasMol ]
		Ala B:776 - Tyr B:777	[ RasMol ]
		Asn A:734 - Gly A:735	[ RasMol ]
		Gly A:718 - Pro A:719	[ RasMol ]
		Gly B:718 - Pro B:719	[ RasMol ]

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	2w20
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Description

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Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

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