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(-) Description

Title :  CONTRIBUTION OF THE ACTIVE SITE ASPARTIC ACID TO CATALYSIS IN THE BACTERIAL NEURAMINIDASE FROM MICROMONOSPORA VIRIDIFACIENS.
 
Authors :  S. Newstead, J. N. Watson, V. Dookhun, A. J. Bennet, G. Taylor
Date :  24 Sep 04  (Deposition) - 30 Sep 04  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosidase, Hydrolase, Neuraminidase, Beta- Propeller Fold. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Watson, S. Newstead, V. Dookhun, G. Taylor, A. J. Bennet
Contribution Of The Active Site Aspartic Acid To Catalysis In The Bacterial Neuraminidase From Micromonospora Viridifaciens
Febs Lett. V. 577 265 2004
PubMed-ID: 15527797  |  Reference-DOI: 10.1016/J.FEBSLET.2004.10.016

(-) Compounds

Molecule 1 - BACTERIAL SIALIDASE
    Atcc: 31146
    Chains: A
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 47-647
    Mutation: YES
    Organism Scientific: MICROMONOSPORA VIRIDIFACIENS
    Organism Taxid: 1881

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2GAL1Ligand/IonBETA-D-GALACTOSE
3NA1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:522 , HIS A:539 , TRP A:542 , ARG A:572 , HOH A:2435 , HOH A:2513BINDING SITE FOR RESIDUE GAL A1648
2AC2SOFTWAREASN A:528 , ASP A:531 , ASN A:533 , THR A:536 , ALA A:639BINDING SITE FOR RESIDUE NA A1650
3AC3SOFTWAREARG A:68 , ILE A:69 , ARG A:87 , ASP A:131 , PHE A:155 , PHE A:203 , PHE A:234 , ASP A:259 , ARG A:276 , ARG A:342 , TYR A:370 , HOH A:2063 , HOH A:2514 , HOH A:2515 , HOH A:2516BINDING SITE FOR RESIDUE DAN A1649

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:351 -A:405

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:93 -Pro A:94
2Ala A:124 -Pro A:125
3Tyr A:550 -Pro A:551
4Gly A:596 -Pro A:597

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W8N)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.NANH_MICVI496-646  1A:496-646

(-) Exons   (0, 0)

(no "Exon" information available for 1W8N)

(-) 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:601
 aligned with NANH_MICVI | Q02834 from UniProtKB/Swiss-Prot  Length:647

    Alignment length:601
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646 
           NANH_MICVI    47 GEPLYTEQDLAVNGREGFPNYRIPALTVTPDGDLLASYDGRPTGIDAPGPNSILQRRSTDGGRTWGEQQVVSAGQTTAPIKGFSDPSYLVDRETGTIFNFHVYSQRQGFAGSRPGTDPADPNVLHANVATSTDGGLTWSHRTITADITPDPGWRSRFAASGEGIQLRYGPHAGRLIQQYTIINAAGAFQAVSVYSDDHGRTWRAGEAVGVGMDENKTVELSDGRVLLNSRDSARSGYRKVAVSTDGGHSYGPVTIDRDLPDPTNNASIIRAFPDAPAGSARAKVLLFSNAASQTSRSQGTIRMSCDDGQTWPVSKVFQPGSMSYSTLTALPDGTYGLLYEPGTGIRYANFNLAWLGGICAPFTIPDVALEPGQQVTVPVAVTNQSGIAVPKPSLQLDASPDWQVQGSVEPLMPGRQAKGQVTITVPAGTTPGRYRVGATLRTSAGNASTTFTVTVGLLDQARMSIADVDSEETAREDGRASNVIDGNPSTFWHTEWSRADAPGYPHRISLDLGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTWDGPVASGRFTTSLAPQRAVFPARDARYIRLVALSEQTGHKYAAVAELEVEGQR 647
               SCOP domains d1w8na3 A:47-402 Micromonospora sialidase, N-terminal domain                                                                                                                                                                                                                                                                                                        d1w8na1 A:403-505 Sialidase, linker domain                                                             d1w8na2 A:506-647 Sialidase, C-terminal domain                                                                                                 SCOP domains
               CATH domains 1w8nA01 A:47-400  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                             1w8nA02 A:401-502 Immunoglobulins                                                                     1w8nA03 A:503-647 Galactose-binding domain-like                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NPCBM_assoc-1w8nA01 A:415-489                                              ----------------------F5_F8_type_C-1w8nA02 A:512-641                                                                                                    ------ Pfam domains
         Sec.struct. author ....eeeeeeee........eeeeeeee.....eeeeeee...........eeeeeee..........eeee.........eeeeeeeee......eeeeeeee....................eeeeeee.......eeee.hhhh.......eeee..ee.ee.........eeeeeeee.....eeeeeeee.......ee..........eeeee.....eeeee.......eeeeeee..........eeeeeee......eeee........hhhhh.eeeeee......eeeeeeee........eeeeeeeee...eeeee.....eeeee....eeeeeeehhhhhh.....ee...eee....eeeeeeeee..........eeeee.....eeeeee.......eeeeeeeee.......eeeeeeeeee.....eeeeeeeee...hhhhheeeee..........hhhhhhh......ee............eeeeeeeeeeeeeeeeeeee..........eeeeeee......eeeeeeee.......eeeeeeeeeeeeeeeee..........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FA58C_3  PDB: A:496-646 UniProt: 496-646                                                                                                               - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w8n A  47 GEPLYTEQDLAVNGREGFPNYRIPALTVTPDGDLLASYDGRPTGIGAPGPNSILQRRSTDGGRTWGEQQVVSAGQTTAPIKGFSDPSYLVDRETGTIFNFHVYSQRQGFAGSRPGTDPADPNVLHANVATSTDGGLTWSHRTITADITPDPGWRSRFAASGEGIQLRYGPHAGRLIQQYTIINAAGAFQAVSVYSDDHGRTWRAGEAVGVGMDENKTVELSDGRVLLNSRDSARSGYRKVAVSTDGGHSYGPVTIDRDLPDPTNNASIIRAFPDAPAGSARAKVLLFSNAASQTSRSQGTIRMSCDDGQTWPVSKVFQPGSMSYSTLTALPDGTYGLLYEPGTGIRYANFNLAWLGGICAPFTIPDVALEPGQQVTVPVAVTNQSGIAVPKPSLQLDASPDWQVQGSVEPLMPGRQAKGQVTITVPAGTTPGRYRVGATLRTSAGNASTTFTVTVGLLDQARMSIADVDSEETAREDGRASNVIDGNPSTFWHTEWSRADAPGYPHRISLDLGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTWDGPVASGRFTTSLAPQRAVFPARDARYIRLVALSEQTGHKYAAVAELEVEGQR 647
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646
   Legend:   → Mismatch (orange background)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)
(-)
Clan: GBD (153)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NANH_MICVI | Q02834)
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: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: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.

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  1w8n
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  NANH_MICVI | Q02834
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  3.2.1.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        NANH_MICVI | Q02834: 1eur 1eus 1eut 1euu 1w8o 1wcq 2ber 2bzd 4j9t

(-) Related Entries Specified in the PDB File

1eur SIALIDASE
1eus SIALIDASE COMPLEXED WITH 2-DEOXY-2,3- DEHYDRO-N- ACETYLNEURAMINIC ACID
1eut SIALIDASE, LARGE 68KD FORM, COMPLEXED WITH GALACTOSE
1euu SIALIDASE OR NEURAMINIDASE, LARGE 68KD FORM