2VK7 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

Authors :   S. L. Newstead, J. A. Potter, J. C. Wilson, G. Xu, C. H. Chien, A. G. Watts, S. G. Withers, G. L. Taylor

Date :   17 Dec 07 (Deposition) - 22 Jan 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

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

Keywords :   Hydrolase, Sialidase, Glycosidase, Sialic Acid, Clostridium Perfringens (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. L. Newstead, J. A. Potter, J. C. Wilson, G. Xu, C. H. Chien, A. G. Watts, S. G. Withers, G. L. Taylor
The Structure Of Clostridium Perfringens Nani Sialidase And Its Catalytic Intermediates.
J. Biol. Chem. V. 283 9080 2008
PubMed-ID: 18218621 | Reference-DOI: 10.1074/JBC.M710247200

Molecule 1 - EXO-ALPHA-SIALIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 243-694
	Organism Scientific	:	CLOSTRIDIUM PERFRINGENS
	Organism Taxid	:	1502
	Synonym	:	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 (2, 6)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	FSI	2	Ligand/Ion	5-(ACETYLAMINO)-2,6-ANHYDRO-3,5-DIDEOXY-3-FLUORONONONIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	FSI	1	Ligand/Ion	5-(ACETYLAMINO)-2,6-ANHYDRO-3,5-DIDEOXY-3-FLUORONONONIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	FSI	1	Ligand/Ion	5-(ACETYLAMINO)-2,6-ANHYDRO-3,5-DIDEOXY-3-FLUORONONONIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:1515 , TRP A:1573 , HOH A:3221 , HOH A:3559 , HOH A:3562 , HOH A:3566	BINDING SITE FOR RESIDUE CA A2692
2	AC2	SOFTWARE	ARG A:1266 , ILE A:1267 , ARG A:1285 , ASP A:1291 , ILE A:1327 , ASP A:1328 , PHE A:1353 , TYR A:1485 , GLN A:1493 , ARG A:1555 , TYR A:1587 , ARG A:1615 , TYR A:1655 , HOH A:3128 , HOH A:3612 , HOH A:3625 , HOH A:3883 , HOH A:3885 , HOH A:3886	BINDING SITE FOR RESIDUE FSI A2693
3	AC3	SOFTWARE	ARG B:1266 , ILE B:1267 , ARG B:1285 , ASP B:1291 , ILE B:1327 , ASP B:1328 , PHE B:1353 , TYR B:1485 , GLN B:1493 , ARG B:1555 , TYR B:1587 , ARG B:1615 , TYR B:1655 , HOH B:3111 , HOH B:3516 , HOH B:3773 , HOH B:3775	BINDING SITE FOR RESIDUE FSI B2692
4	AC4	SOFTWARE	ASP B:1515 , TRP B:1573 , HOH B:3201 , HOH B:3479 , HOH B:3480 , HOH B:3482	BINDING SITE FOR RESIDUE CA B2693
5	AC5	SOFTWARE	ASP A:1296 , ASP A:1298 , ASP A:1319 , TYR A:1320 , HOH A:3142 , HOH A:3144 , HOH A:3145	BINDING SITE FOR RESIDUE CA A2694
6	AC6	SOFTWARE	ASP B:1296 , ASP B:1298 , ASP B:1319 , TYR B:1320 , HOH B:3126 , HOH B:3129 , HOH B:3215	BINDING SITE FOR RESIDUE CA B2694

(no "SS Bond" information available for 2VK7)

Asymmetric Unit

No.	Residues
1	Ala A:1292	-	Pro A:1293
2	Ala B:1292	-	Pro B:1293

(no "SAP(SNP)/Variant" information available for 2VK7)

(no "PROSITE Motif" information available for 2VK7)

(no "Exon" information available for 2VK7)

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:449
 aligned with Q59310_CLOPF | Q59310 from UniProtKB/TrEMBL  Length:694

    Alignment length:449
                                   252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682         
        Q59310_CLOPF    243 VEGAVKTEPVDLFHPGFLNSSNYRIPALFKTKEGTLIASIDARRHGGADAPNNDIDTAVRRSEDGGKTWDEGQIIMDYPDKSSVIDTTLIQDDETGRIFLLVTHFPSKYGFWNAGLGSGFKNIDGKEYLCLYDSSGKEFTVRENVVYDKDGNKTEYTTNALGDLFKNGTKIDNINSSTAPLKAKGTSYINLVYSDDDGKTWSEPQNINFQVKKDWMKFLGIAPGRGIQIKNGEHKGRIVVPVYYTNEKGKQSSAVIYSDDSGKNWTIGESPNDNRKLENGKIINSKTLSDDAPQLTECQVVEMPNGQLKLFMRNLSGYLNIATSFDGGATWDETVEKDTNVLEPYCQLSVINYSQKVDGKDAVIFSNPNARSRSNGTVRIGLINQVGTYENGEPKYEFDWKYNKLVKPGYYAYSCLTELSNGNIGLLYEGTPSEEMSYIEMNLKYLESG  691
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vk7A01 A:1243-1360,A:1427-1691  [code=2.120.10.10, no name defined]                                                  ------------------------------------------------------------------2vk7A01 A:1243-1360,A:1427-1691  [code=2.120.10.10, no name defined]                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..hhhhh.eeeeeeeee.....eeeeeeee...........eeeeeeee..........eeee......eeeeeeeeee....eeeeeeeee..............eeee..eeeeeee.....eeeee..eee.....eeeeee....eeee..eeeee........ee....eeeeeee..........eehhhhhh......eee..ee.ee.........eeeeeeee.....eeeeeeee.......ee.......ee.....ee...........eeeeeeee.....eeeeeee...eeeeeee...........eeeeeee......eeee.........eeeeeee.....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee...eeeee.....eeeeee......eeeeeehhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vk7 A 1243 VEGAVKTEPVDLFHPGFLNSSNYRIPALFKTKEGTLIASIDARRHGGADAPNNDIDTAVRRSEDGGKTWDEGQIIMDYPDKSSVIDTTLIQDDETGRIFLLVTHFPSKYGFWNAGLGSGFKNIDGKEYLCLYDSSGKEFTVRENVVYDKDSNKTEYTTNALGDLFKNGTKIDNINSSTAPLKAKGTSYINLVYSDDDGKTWSEPQNINFQVKKDWMKFLGIAPGRGIQIKNGEHKGRIVVPVYYTNEKGKQSSAVIYSDDSGKNWTIGESPNDNRKLENGKIINSKTLSDDAPQLTECQVVEMPNGQLKLFMRNLSGYLNIATSFDGGATWDETVEKDTNVLEPYCQLSVINYSQKVDGKDAVIFSNPNARSRSNGTVRIGLINQVGTYENGEPKYEFDWKYNKLVKPGYYAYSCLTELSNGNIGLLYEGTPSEEMSYIEMNLKYLESG 1691
                                  1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402      1412      1422      1432      1442      1452      1462      1472      1482      1492      1502      1512      1522      1532      1542      1552      1562      1572      1582      1592      1602      1612      1622      1632      1642      1652      1662      1672      1682

Chain B from PDB  Type:PROTEIN  Length:449
 aligned with Q59310_CLOPF | Q59310 from UniProtKB/TrEMBL  Length:694

    Alignment length:449
                                   252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682         
        Q59310_CLOPF    243 VEGAVKTEPVDLFHPGFLNSSNYRIPALFKTKEGTLIASIDARRHGGADAPNNDIDTAVRRSEDGGKTWDEGQIIMDYPDKSSVIDTTLIQDDETGRIFLLVTHFPSKYGFWNAGLGSGFKNIDGKEYLCLYDSSGKEFTVRENVVYDKDGNKTEYTTNALGDLFKNGTKIDNINSSTAPLKAKGTSYINLVYSDDDGKTWSEPQNINFQVKKDWMKFLGIAPGRGIQIKNGEHKGRIVVPVYYTNEKGKQSSAVIYSDDSGKNWTIGESPNDNRKLENGKIINSKTLSDDAPQLTECQVVEMPNGQLKLFMRNLSGYLNIATSFDGGATWDETVEKDTNVLEPYCQLSVINYSQKVDGKDAVIFSNPNARSRSNGTVRIGLINQVGTYENGEPKYEFDWKYNKLVKPGYYAYSCLTELSNGNIGLLYEGTPSEEMSYIEMNLKYLESG  691
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vk7B01 B:1243-1360,B:1427-1691  [code=2.120.10.10, no name defined]                                                  ------------------------------------------------------------------2vk7B01 B:1243-1360,B:1427-1691  [code=2.120.10.10, no name defined]                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..hhhhh.eeeeeeeee.....eeeeeeee...........eeeeeeee..........eeee......eeeeeeeee......eeeeeeee..............eeee..eeeeeee.....eeeee..eee.....eeeeee....eeee..eeeee........ee....eeeeeee..........eehhhhhh......eee..ee.ee.........eeeeeeee.....eeeeeeee.......ee.......ee.....ee...........eeeeeeee.....eeeeeee...eeeeeee...........eeeeeee......eeeeeeeee..eeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee...eeeee.....eeeeee......eeeeeehhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vk7 B 1243 VEGAVKTEPVDLFHPGFLNSSNYRIPALFKTKEGTLIASIDARRHGGADAPNNDIDTAVRRSEDGGKTWDEGQIIMDYPDKSSVIDTTLIQDDETGRIFLLVTHFPSKYGFWNAGLGSGFKNIDGKEYLCLYDSSGKEFTVRENVVYDKDSNKTEYTTNALGDLFKNGTKIDNINSSTAPLKAKGTSYINLVYSDDDGKTWSEPQNINFQVKKDWMKFLGIAPGRGIQIKNGEHKGRIVVPVYYTNEKGKQSSAVIYSDDSGKNWTIGESPNDNRKLENGKIINSKTLSDDAPQLTECQVVEMPNGQLKLFMRNLSGYLNIATSFDGGATWDETVEKDTNVLEPYCQLSVINYSQKVDGKDAVIFSNPNARSRSNGTVRIGLINQVGTYENGEPKYEFDWKYNKLVKPGYYAYSCLTELSNGNIGLLYEGTPSEEMSYIEMNLKYLESG 1691
                                  1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402      1412      1422      1432      1442      1452      1462      1472      1482      1492      1502      1512      1522      1532      1542      1552      1562      1572      1582      1592      1602      1612      1622      1632      1642      1652      1662      1672      1682

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 2VK7)

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)

Clostridium perfringens. Organism_taxid: 1502. (3)

1a	2vk7A01	A:1243-1360,A:1427-1691
1b	2vk7B01	B:1243-1360,B:1427-1691

(no "Pfam Domain" information available for 2VK7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q59310_CLOPF | Q59310)

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.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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 Unit
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	Cis Peptide Bonds
		Ala A:1292 - Pro A:1293	[ RasMol ]
		Ala B:1292 - Pro B:1293	[ RasMol ]

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	2vk7
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	Q59310_CLOPF \| Q59310
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	3.2.1.18
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	Q59310_CLOPF \| Q59310	:	2bf6 2vk5 2vk6

2bf6	ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA-SIALIC ACID (NEU5AC).
2vk5	THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES
2vk6	THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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