2VVZ - JenaLib

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Biological Unit 2 (Jmol Viewer)

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

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

Date :   13 Jun 08 (Deposition) - 24 Jun 08 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Secreted, Cell Wall, Sialidase, Hydrolase, Peptidoglycan-Anchor, Glycosidase, Neuraminidase, Virulence Factor (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 319-822
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Strain	:	R36A
	Synonym	:	NANA SIALIDASE, NEURAMINIDASE A

		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 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	DAN	2	Ligand/Ion	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DAN	1	Ligand/Ion	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DAN	1	Ligand/Ion	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:347 , ILE A:348 , ARG A:366 , ASP A:372 , ILE A:416 , ASP A:417 , ASP A:434 , ILE A:442 , TYR A:590 , LEU A:598 , GLN A:602 , ARG A:663 , TYR A:695 , ARG A:721 , TYR A:752 , HOH A:2094	BINDING SITE FOR RESIDUE DAN A1792
2	AC2	SOFTWARE	ARG B:347 , ILE B:348 , ARG B:366 , ASP B:372 , ILE B:416 , ASP B:417 , ASP B:434 , ILE B:442 , TYR B:590 , GLN B:602 , ARG B:663 , TYR B:695 , ARG B:721 , TYR B:752	BINDING SITE FOR RESIDUE DAN B1792
3	AC3	SOFTWARE	GLY A:516 , ASN A:517 , PHE A:520 , LYS A:524 , THR A:525 , SER A:526	BINDING SITE FOR RESIDUE CL A1793

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

Asymmetric Unit

No.	Residues
1	Lys A:708	-	Glu A:709
2	Gly A:718	-	Pro A:719
3	Asn A:734	-	Gly A:735
4	Ala A:776	-	Tyr A:777
5	Gly B:458	-	Lys B:459
6	Lys B:708	-	Glu B:709
7	Gly B:718	-	Pro B:719
8	Asn B:734	-	Gly B:735
9	Ala B:776	-	Tyr B:777
10	Asn B:785	-	Trp B:786

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

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

(no "Exon" information available for 2VVZ)

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_STREE | P62575 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:470
                                   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       791
           NANA_STREE   322 ALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSK 791
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vvzA01 A:322-451,A:532-791  [code=2.120.10.10, no name defined]                                                                  --------------------------------------------------------------------------------2vvzA01 A:322-451,A:532-791  [code=2.120.10.10, no name defined]                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..............ee...eeee.....eeeeeeee.........eeeeeeee..........eeee................eeeeeeeee......eeeeeeee................eeee..eeee..ee..........................ee............eee.....eee..........ee.....eeeeeee..........eehhhhhh......eee..ee.ee.........eeeeeee...........eeeeeee.......ee.......eee..eee..............eeeee.....eeeee.....eeeeeee...........eeeeeee......eeee........eeeeee.....eeeeeeeeee.....eeeeeeeeeeeee...eeeeeee..eeeeeeee........eeeeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvz A 322 ALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSK 791
                                   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       791

Chain B from PDB  Type:PROTEIN  Length:470
 aligned with NANA_STREE | P62575 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:470
                                   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       791
           NANA_STREE   322 ALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSK 791
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vvzB01 B:322-451,B:532-791  [code=2.120.10.10, no name defined]                                                                  --------------------------------------------------------------------------------2vvzB01 B:322-451,B:532-791  [code=2.120.10.10, no name defined]                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee................eeeeeeeee.....eeeeeeee.........eeeeeeee..........eeee.........hhhhh..eeeeeeeee......eeeeeeee................eee....eeeeeee.......ee....eee.....eeeeeee............eeee..eeeee..........eee....eeeeeee..........eehhhhhh......eee..ee.ee..hhhhh..eeeeeee....hhhhhh.eeeeeee.......ee.......eee..eee..............eeeee.....eeeee.....eeeeeee...........eeeeeee......eeee........eeeee......eeeeeeeeee.....eeeeeeeeeeeeeeeeeeeeeee..eeeeeeee..........eeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvz B 322 ALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSK 791
                                   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       791

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 2VVZ)

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: 1313. Strain: r36a. (1)

1a	2vvzA01	A:322-451,A:532-791
1b	2vvzB01	B:322-451,B:532-791

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (NANA_STREE | P62575)

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.
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: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: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 ]
		Asn B:734 - Gly B:735	[ RasMol ]
		Asn B:785 - Trp B:786	[ RasMol ]
		Gly A:718 - Pro A:719	[ RasMol ]
		Gly B:458 - Lys B:459	[ RasMol ]
		Gly B:718 - Pro B:719	[ RasMol ]
		Lys A:708 - Glu A:709	[ RasMol ]
		Lys B:708 - Glu B:709	[ RasMol ]

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	2vvz
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	3.2.1.18
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	NANA_STREE \| P62575	:	2ya4 2ya5 2ya6 2ya7 2ya8 4c1x 4zxk 5kky

(no "Related Entries Specified in the PDB File" available for 2VVZ)

Description

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Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

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