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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN SIALIDASE NEU2 Q116E MUTANT
 
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 :  1.67
Chains :  Asym./Biol. Unit :  A
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 Q116E Mutant
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIALIDASE 2
    ChainsA
    EC Number3.2.1.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEU2, CYTOSOLIC SIALIDASE, N-ACETYL-ALPHA- NEURAMINIDASE 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:28 , GLY A:30 , GLN A:31 , HOH A:1077 , HOH A:1268BINDING SITE FOR RESIDUE CL A 1001
2AC2SOFTWAREHOH A:1012BINDING SITE FOR RESIDUE CL A 1002

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:88 -A:164

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:160 -Pro A:161
2Pro A:268 -Pro A:269
3Pro A:315 -Pro A:316

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024461S11RNEUR2_HUMANPolymorphism2233384AS11R
2UniProtVAR_024462R41QNEUR2_HUMANPolymorphism2233385AR41Q
3UniProtVAR_049204A145TNEUR2_HUMANPolymorphism2233390AA145T
4UniProtVAR_055311H168NNEUR2_HUMANPolymorphism2233391AN168N
5UniProtVAR_055312R182QNEUR2_HUMANPolymorphism2233393AR182Q

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F28)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002338401ENSE00001709784chr2:233897382-233897582201NEUR2_HUMAN1-67671A:5-67 (gaps)63
1.2ENST000002338402ENSE00000786879chr2:233898826-233899767942NEUR2_HUMAN68-3803131A:68-377 (gaps)310

(-) Sequences/Alignments

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:358
 aligned with NEUR2_HUMAN | Q9Y3R4 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:373
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374   
          NEUR2_HUMAN     5 PVLQKESVFQSGAHAYRIPALLYLPGQQSLLAFAEQRASKKDEHAELIVLRRGDYDAPTHQVQWQAQEVVAQARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTEQQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLHDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLVKKLVEPPPQGCQGSVISFPSPRSGPGSPAQWLLYTHPTHSWQRADLGAYLNPRPPAPEAWSEPVLLAKGSCAYSDLQSMGTGPDGSPLFGCLYEANDYEEIVFLMFTLKQAFPAEY 377
               SCOP domains d2f28a_ A: Sialidase 2 (Neu2)                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....eeeeeeeee....eeeeeeee.--------.eeeeeeeeee....eeee...ee........eeeeeeeeee......eeeeeeeee...hhhhhhh......eeeeeee..........eehhhhhhhhhhh.eeeeee.....ee.......eeeeeeeee........eeeeeeeee.......ee.......eeeeeeeee.---..eeeeeeee...eeeeeee..........eeeeeee.........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:5-67 (gaps) UniProt: 1-67 [INCOMPLETE]        Exon 1.2  PDB: A:68-377 (gaps) UniProt: 68-380 [INCOMPLETE]                                                                                                                                                                                                                                                            Transcript 1
                 2f28 A   5 PVLQKESVFQSGAHAYRIPALLYLPGQQSLLAFAEQR--------ELIVLRRGDYDAPTHQVQWQAQEVVAQARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTEQQQLETRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVE---QRVVTLNARSHLRARVQAQSTNDGLDFQESQLVKKLVEPPPQGCQGSVISFPSPR----SPAQWLLYTHPTHSWQRADLGAYLNPRPPAPEAWSEPVLLAKGSCAYSDLQSMGTGPDGSPLFGCLYEANDYEEIVFLMFTLKQAFPAEY 377
                                    14        24        34      |  -     |  54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224|   |  234       244       254       264       274        |-   |   294       304       314       324       334       344       354       364       374   
                                                               41       50                                                                                                                                                                            225 229                                                   283  288                                                                                         

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F28)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F28)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NEUR2_HUMAN | Q9Y3R41snt 1so7 1vcu 2f0z 2f10 2f11 2f12 2f13 2f24 2f25 2f26 2f27 2f29 4nc5 4ncs

(-) Related Entries Specified in the PDB File

1snt HUMAN NEU2 APO-FORM
1so7 HUMAN NEU2 SUGAR-INDUCED FORM
1vcu HUMAN NEU2-DANA COMPLEX
2f0z
2f10
2f11
2f12
2f13
2f24
2f25
2f26
2f27
2f29