2F25 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN SIALIDASE NEU2 E111Q MUTANT IN COMPLEX WITH DANA INHIBITOR

Authors :   L. M. G. Chavas, R. Kato, P. Fusi, C. Tringali, B. Venerando, G. Tettamanti, E. Monti, S. Wakatsuki

Date :   15 Nov 05 (Deposition) - 21 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

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

Reference :   L. M. G. Chavas, R. Kato, P. Fusi, C. Tringali, B. Venerando, G. Tettamanti, E. Monti, S. Wakatsuki
Crystal Structure Of The Human Sialidase Neu2 E111Q Mutant In Complex With Dana Inhibitor
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SIALIDASE 2
	Chains	:	A, B
	EC Number	:	3.2.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NEU2, CYTOSOLIC SIALIDASE, N-ACETYL-ALPHA- NEURAMINIDASE 2

		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	DAN	2	Ligand/Ion	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2	EPE	4	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	DAN	1	Ligand/Ion	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	DAN	1	Ligand/Ion	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:21 , ASP A:46 , GLN A:111 , TYR A:179 , TYR A:181 , GLU A:218 , ARG A:237 , ARG A:304 , TYR A:334 , EPE A:1005 , HOH A:1019 , HOH A:1031 , HOH A:1033 , HOH A:1132 , HOH A:1193	BINDING SITE FOR RESIDUE DAN A 1001
2	AC2	SOFTWARE	ARG B:21 , ARG B:41 , ASP B:46 , MET B:85 , GLN B:111 , TYR B:179 , TYR B:181 , GLU B:218 , ARG B:237 , GLN B:270 , ARG B:304 , TYR B:334 , HOH B:1047 , HOH B:1056 , HOH B:1061 , HOH B:1107 , HOH B:1115	BINDING SITE FOR RESIDUE DAN B 1002
3	AC3	SOFTWARE	SER A:11 , VAL A:12 , PHE A:13 , GLN A:14 , GLY A:16 , ALA A:17 , HIS A:18 , TYR A:20 , ARG A:55 , HOH A:1006 , HOH A:1016 , HOH A:1126 , HOH A:1166 , VAL B:6 , LEU B:7	BINDING SITE FOR RESIDUE EPE A 1003
4	AC4	SOFTWARE	VAL A:6 , LEU A:7 , HOH A:1034 , SER B:11 , VAL B:12 , PHE B:13 , GLN B:14 , GLY B:16 , ALA B:17 , HIS B:18 , TYR B:20 , HOH B:1007	BINDING SITE FOR RESIDUE EPE B 1004
5	AC5	SOFTWARE	ARG A:21 , ARG A:41 , LYS A:44 , ASP A:46 , ARG A:237 , PRO A:269 , GLN A:270 , ARG A:304 , TYR A:359 , DAN A:1001 , HOH A:1033 , HOH A:1046 , HOH A:1077	BINDING SITE FOR RESIDUE EPE A 1005
6	AC6	SOFTWARE	ARG B:21 , ARG B:41 , LYS B:44 , ASP B:46 , PRO B:269 , GLN B:270 , TYR B:359 , HOH B:1047 , HOH B:1063 , HOH B:1096	BINDING SITE FOR RESIDUE EPE B 1006

(no "SS Bond" information available for 2F25)

Asymmetric Unit

No.	Residues
1	Gly A:160	-	Pro A:161
2	Pro A:268	-	Pro A:269
3	Pro A:315	-	Pro A:316
4	Gly B:160	-	Pro B:161
5	Pro B:268	-	Pro B:269
6	Pro B:315	-	Pro B:316

Asymmetric Unit (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024461	S	11	R	NEUR2_HUMAN	Polymorphism	2233384	A/B	S	11	R
2	UniProt	VAR_024462	R	41	Q	NEUR2_HUMAN	Polymorphism	2233385	A/B	R	41	Q
3	UniProt	VAR_049204	A	145	T	NEUR2_HUMAN	Polymorphism	2233390	A/B	A	145	T
4	UniProt	VAR_055311	H	168	N	NEUR2_HUMAN	Polymorphism	2233391	A/B	N	168	N
5	UniProt	VAR_055312	R	182	Q	NEUR2_HUMAN	Polymorphism	2233393	A/B	R	182	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024461	S	11	R	NEUR2_HUMAN	Polymorphism	2233384	A	S	11	R
2	UniProt	VAR_024462	R	41	Q	NEUR2_HUMAN	Polymorphism	2233385	A	R	41	Q
3	UniProt	VAR_049204	A	145	T	NEUR2_HUMAN	Polymorphism	2233390	A	A	145	T
4	UniProt	VAR_055311	H	168	N	NEUR2_HUMAN	Polymorphism	2233391	A	N	168	N
5	UniProt	VAR_055312	R	182	Q	NEUR2_HUMAN	Polymorphism	2233393	A	R	182	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024461	S	11	R	NEUR2_HUMAN	Polymorphism	2233384	B	S	11	R
2	UniProt	VAR_024462	R	41	Q	NEUR2_HUMAN	Polymorphism	2233385	B	R	41	Q
3	UniProt	VAR_049204	A	145	T	NEUR2_HUMAN	Polymorphism	2233390	B	A	145	T
4	UniProt	VAR_055311	H	168	N	NEUR2_HUMAN	Polymorphism	2233391	B	N	168	N
5	UniProt	VAR_055312	R	182	Q	NEUR2_HUMAN	Polymorphism	2233393	B	R	182	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2F25)

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000233840	1	ENSE00001709784	chr2:233897382-233897582	201	NEUR2_HUMAN	1-67	67	2	A:1-67 B:1-67	67 67
1.2	ENST00000233840	2	ENSE00000786879	chr2:233898826-233899767	942	NEUR2_HUMAN	68-380	313	2	A:68-377 (gaps) B:68-377 (gaps)	310 310

Asymmetric Unit

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	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:373
 aligned with NEUR2_HUMAN | Q9Y3R4 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:377
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       
          NEUR2_HUMAN     1 MASLPVLQKESVFQSGAHAYRIPALLYLPGQQSLLAFAEQRASKKDEHAELIVLRRGDYDAPTHQVQWQAQEVVAQARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTEQQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLHDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLVKKLVEPPPQGCQGSVISFPSPRSGPGSPAQWLLYTHPTHSWQRADLGAYLNPRPPAPEAWSEPVLLAKGSCAYSDLQSMGTGPDGSPLFGCLYEANDYEEIVFLMFTLKQAFPAEY 377
               SCOP domains d2f25a_ A: Sialidase 2 (Neu2)                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee....eeeeeeeeee....eeeeeeeee...hhh.eeeeeeeeeeee....eeee...ee........eeeeeeeeeee....eeeeeeeeee...hhhhhhhhh....eeeeeee..........eehhhhhhhhhhh.eeeeee.....ee.......eeeeeeeee........eeeeeeeee.......ee..........eeeeeee....eeeeeee.....eeeeeee.......eeeeeeeeee.........eeeeee...----...eeeeeeee......eeeeeeee....hhhhh...eeeeeeeeeeeeeeeeee.....eeeeeeeee....eeeeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------R-----------------------------Q-------------------------------------------------------------------------------------------------------T----------------------N-------------Q--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-67 UniProt: 1-67                                Exon 1.2  PDB: A:68-377 (gaps) UniProt: 68-380 [INCOMPLETE]                                                                                                                                                                                                                                                            Transcript 1
                 2f25 A   1 MASLPVLQKESVFQSGAHAYRIPALLYLPGQQSLLAFAEQRASKKDEHAELIVLRRGDYDAPTHQVQWQAQEVVAQARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTQQQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLVKKLVEPPPQGCQGSVISFPSPR----SPAQWLLYTHPTHSWQRADLGAYLNPRPPAPEAWSEPVLLAKGSCAYSDLQSMGTGPDGSPLFGCLYEANDYEEIVFLMFTLKQAFPAEY 377
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  |    290       300       310       320       330       340       350       360       370       
                                                                                                                                                                                                                                                                                                                    283  288

Chain B from PDB  Type:PROTEIN  Length:370
 aligned with NEUR2_HUMAN | Q9Y3R4 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:377
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       
          NEUR2_HUMAN     1 MASLPVLQKESVFQSGAHAYRIPALLYLPGQQSLLAFAEQRASKKDEHAELIVLRRGDYDAPTHQVQWQAQEVVAQARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTEQQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLHDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLVKKLVEPPPQGCQGSVISFPSPRSGPGSPAQWLLYTHPTHSWQRADLGAYLNPRPPAPEAWSEPVLLAKGSCAYSDLQSMGTGPDGSPLFGCLYEANDYEEIVFLMFTLKQAFPAEY 377
               SCOP domains d2f25b_ B: Sialidase 2 (Neu2)                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee....eeeeeeeeee....eeeeeeeee...hhh.eeeeeeeeeeee....eeee...ee........eeeeeeeeee......eeeeeeeee...hhhhhhhhh....eeeeeee..........eehhhhhhhhhhh.eeeeee.....ee.......eeeeeeeee........eeeeeeeee.......ee..........eeeeee.---..eeeeee.....eeeeeee........eeeeeeeee.........eeeeee...----...eeeeeeee......eeeeeeee....hhhhh...eeeeeeeeeeeeeeeeee.....eeeeeeeee....eeeeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------R-----------------------------Q-------------------------------------------------------------------------------------------------------T----------------------N-------------Q--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-67 UniProt: 1-67                                Exon 1.2  PDB: B:68-377 (gaps) UniProt: 68-380 [INCOMPLETE]                                                                                                                                                                                                                                                            Transcript 1
                 2f25 B   1 MASLPVLQKESVFQSGAHAYRIPALLYLPGQQSLLAFAEQRASKKDEHAELIVLRRGDYDAPTHQVQWQAQEVVAQARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTQQQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVE---QRVVTLNARSHLRARVQAQSTNDGLDFQESQLVKKLVEPPPQGCQGSVISFPSPR----SPAQWLLYTHPTHSWQRADLGAYLNPRPPAPEAWSEPVLLAKGSCAYSDLQSMGTGPDGSPLFGCLYEANDYEEIVFLMFTLKQAFPAEY 377
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    |  230       240       250       260       270       280  |    290       300       310       320       330       340       350       360       370       
                                                                                                                                                                                                                                                          225 229                                                   283  288

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	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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: All beta proteins (24004)

Fold: 6-bladed beta-propeller (327)

Superfamily: Sialidases (238)

Family: Sialidases (neuraminidases) (178)

Protein domain: Sialidase 2 (Neu2) (14)

Human (Homo sapiens) [TaxId: 9606] (14)

1a	d2f25a_	A:
1b	d2f25b_	B:

(no "CATH Domain" information available for 2F25)

(no "Pfam Domain" information available for 2F25)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NEUR2_HUMAN | Q9Y3R4)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0006687	glycosphingolipid metabolic process	The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide.
	GO:0016042	lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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.
	GO:0045663	positive regulation of myoblast differentiation	Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
	GO:0010831	positive regulation of myotube differentiation	Any process that activates, maintains or increases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
	GO:0045471	response to ethanol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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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		Pro A:268 - Pro A:269	[ RasMol ]
		Pro A:315 - Pro A:316	[ RasMol ]
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		Pro B:315 - Pro B:316	[ RasMol ]

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1snt	HUMAN NEU2 APO-FORM
1so7	HUMAN NEU2 SUGAR-INDUCED FORM
1vcu	HUMAN NEU2-DANA COMPLEX
2f0z
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Description

Compounds

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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