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Protein

Unsaturated chondroitin disaccharide hydrolase

Gene

gbs1889

Organism
Streptococcus agalactiae serotype III (strain NEM316)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the hydrolysis of unsaturated hyaluronate and chondroitin disaccharides. Also degrades unsaturated heparin disaccharides. Releases 4-deoxy-4,5-didehydro D-glucuronic acid or 4-deoxy-4,5-didehydro L-iduronic acid from chondroitin disaccharides, hyaluronan disaccharides and heparin disaccharides and cleaves both glycosidic (1->3) and (1->4) bonds. Prefers sulfated glycosaminoglycans compared to unsulfated glycosaminoglycans. Probably required for mammalian cells invasion through the degradation of extracellular sulfated glycosaminoglycans such as chondroitin and hyaluronan.2 Publications

Catalytic activityi

Beta-D-4-deoxy-Delta(4)-GlcAp-(1->3)-beta-D-GalNAc6S + H2O = 5-dehydro-4-deoxy-D-glucuronate + N-acetyl-beta-D-galactosamine-6-O-sulfate.2 Publications

Kineticsi

kcat is 2.69 sec(-1) with unsaturated chondroitin (delta0S) (PubMed:21147778). kcat is 24 sec(-1) with unsaturated chondroitin disaccharide sulfated at C-6 position of GalNAc residue (delta6S) (PubMed:19416976). kcat is 10.2 sec(-1) with unsaturated chondroitin disaccharide sulfated at C-6 position of GalNAc residue (delta6S) (PubMed:21147778).2 Publications

  1. KM=1.27 mM for unsaturated chondroitin disaccharidee (delta0S)2 Publications
  2. KM=0.1 mM for unsaturated chondroitin disaccharide sulfated at C-6 position of GalNAc residue (delta6S)2 Publications
  3. KM=0.54 mM for unsaturated chondroitin disaccharide sulfated at C-6 position of GalNAc residue (delta6S)1 Publication

    pH dependencei

    Optimum pH is 5.5.1 Publication

    Temperature dependencei

    Optimum temperature is 37 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei115 – 1151Nucleophile1 Publication
    Binding sitei115 – 1151Substrate
    Active sitei175 – 1751Proton donor1 Publication
    Binding sitei175 – 1751Substrate
    Binding sitei233 – 2331Substrate; via carbonyl oxygen
    Binding sitei235 – 2351Substrate
    Binding sitei247 – 2471Substrate
    Binding sitei251 – 2511Substrate
    Binding sitei365 – 3651Substrate
    Binding sitei368 – 3681Substrate

    GO - Molecular functioni

    • chondroitin hydrolase activity Source: UniProtKB

    GO - Biological processi

    • metabolic process Source: UniProtKB
    • pathogenesis Source: UniProtKB
    • polysaccharide catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism, Polysaccharide degradation, Virulence

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16268.
    BRENDAi3.2.1.180. 5917.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Unsaturated chondroitin disaccharide hydrolase (EC:3.2.1.180)
    Alternative name(s):
    Unsaturated glucuronyl hydrolase
    Short name:
    SagUGL
    Gene namesi
    Ordered Locus Names:gbs1889
    OrganismiStreptococcus agalactiae serotype III (strain NEM316)
    Taxonomic identifieri211110 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
    Proteomesi
    • UP000000823 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi115 – 1151D → N: Large decrease in activity. 1 Publication
    Mutagenesisi175 – 1751D → N: Large decrease in activity. 1 Publication
    Mutagenesisi236 – 2361R → A or H: Able to degrade unsaturated chondroitin disaccharide sulfated at C-6 position of GalNAc residue (delta6S) but abolishes ability to degrade unsaturated chondroitin disaccharide sulfated at C-4 position of GalNAc residue (delta4S). 1 Publication
    Mutagenesisi365 – 3651S → H: Prefers unsulfated glycosaminoglycans compared to sulfated glycosaminoglycans. 1 Publication
    Mutagenesisi368 – 3681S → G: Affects preference for sulfated glycosaminoglycans compared to sulfated glycosaminoglycans. 1 Publication
    Mutagenesisi370 – 3701K → I: Prefers unsulfated glycosaminoglycans compared to sulfated glycosaminoglycans. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 398398Unsaturated chondroitin disaccharide hydrolasePRO_0000422016Add
    BLAST

    Expressioni

    Inductioni

    Constitutively expressed. Expression level increases in the presence of glycosaminoglycan.1 Publication

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Protein-protein interaction databases

    STRINGi211110.gbs1889.

    Structurei

    Secondary structure

    1
    398
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi16 – 194Combined sources
    Helixi26 – 4722Combined sources
    Beta strandi50 – 523Combined sources
    Helixi71 – 8515Combined sources
    Helixi88 – 10619Combined sources
    Turni107 – 1104Combined sources
    Helixi113 – 1153Combined sources
    Helixi116 – 1205Combined sources
    Turni121 – 1233Combined sources
    Helixi124 – 1318Combined sources
    Helixi134 – 14916Combined sources
    Helixi176 – 1794Combined sources
    Helixi181 – 19010Combined sources
    Helixi193 – 21018Combined sources
    Turni225 – 2273Combined sources
    Beta strandi238 – 2403Combined sources
    Helixi246 – 26318Combined sources
    Helixi266 – 28116Combined sources
    Beta strandi290 – 2923Combined sources
    Helixi305 – 31915Combined sources
    Helixi329 – 34618Combined sources
    Beta strandi362 – 3654Combined sources
    Turni366 – 3694Combined sources
    Beta strandi370 – 3745Combined sources
    Helixi377 – 39115Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3ANIX-ray2.50A1-398[»]
    3ANJX-ray1.95A1-398[»]
    3ANKX-ray2.02A1-398[»]
    3VXDX-ray2.00A/B/C/D1-398[»]
    3WUXX-ray1.79A1-398[»]
    ProteinModelPortaliQ8E372.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8E372.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 88 family.Curated

    Phylogenomic databases

    eggNOGiENOG4105EP8. Bacteria.
    ENOG410XPY2. LUCA.
    HOGENOMiHOG000217115.
    OMAiYWDLIFG.
    OrthoDBiEOG66XB8V.

    Family and domain databases

    Gene3Di1.50.10.10. 1 hit.
    InterProiIPR008928. 6-hairpin_glycosidase-like.
    IPR012341. 6hp_glycosidase.
    IPR010905. Glyco_hydro_88.
    [Graphical view]
    PfamiPF07470. Glyco_hydro_88. 1 hit.
    [Graphical view]
    SUPFAMiSSF48208. SSF48208. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q8E372-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MMKIKPVKVE SIENPKRFLN SRLLTKIEVE EAIEKALKQL YINIDYFGEE
    60 70 80 90 100
    YPTPATFNNI YKVMDNTEWT NGFWTGCLWL AYEYNQDKKL KNIAHKNVLS
    110 120 130 140 150
    FLNRINNRIA LDHHDLGFLY TPSCTAEYRI NGDVKALEAT IKAADKLMER
    160 170 180 190 200
    YQEKGGFIQA WGELGYKEHY RLIIDCLLNI QLLFFAYEQT GDEKYRQVAV
    210 220 230 240 250
    NHFYASANNV VRDDSSAFHT FYFDPETGEP LKGVTRQGYS DESSWARGQA
    260 270 280 290 300
    WGIYGIPLSY RKMKDYQQII LFKGMTNYFL NRLPEDKVSY WDLIFTDGSG
    310 320 330 340 350
    QPRDTSATAT AVCGIHEMLK YLPEVDPDKE TYKYAMHTML RSLIEQYSNN
    360 370 380 390
    ELIAGRPLLL HGVYSWHSGK GVDEGNIWGD YYYLEALIRF YKDWELYW
    Length:398
    Mass (Da):46,587
    Last modified:March 1, 2003 - v1
    Checksum:i6554A85BE6A0E15D
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL766854 Genomic DNA. Translation: CAD47548.1.
    RefSeqiWP_000975716.1. NC_004368.1.

    Genome annotation databases

    EnsemblBacteriaiCAD47548; CAD47548; CAD47548.
    PATRICi19639701. VBIStrAga3577_1936.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL766854 Genomic DNA. Translation: CAD47548.1.
    RefSeqiWP_000975716.1. NC_004368.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3ANIX-ray2.50A1-398[»]
    3ANJX-ray1.95A1-398[»]
    3ANKX-ray2.02A1-398[»]
    3VXDX-ray2.00A/B/C/D1-398[»]
    3WUXX-ray1.79A1-398[»]
    ProteinModelPortaliQ8E372.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi211110.gbs1889.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAD47548; CAD47548; CAD47548.
    PATRICi19639701. VBIStrAga3577_1936.

    Phylogenomic databases

    eggNOGiENOG4105EP8. Bacteria.
    ENOG410XPY2. LUCA.
    HOGENOMiHOG000217115.
    OMAiYWDLIFG.
    OrthoDBiEOG66XB8V.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16268.
    BRENDAi3.2.1.180. 5917.

    Miscellaneous databases

    EvolutionaryTraceiQ8E372.

    Family and domain databases

    Gene3Di1.50.10.10. 1 hit.
    InterProiIPR008928. 6-hairpin_glycosidase-like.
    IPR012341. 6hp_glycosidase.
    IPR010905. Glyco_hydro_88.
    [Graphical view]
    PfamiPF07470. Glyco_hydro_88. 1 hit.
    [Graphical view]
    SUPFAMiSSF48208. SSF48208. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease."
      Glaser P., Rusniok C., Buchrieser C., Chevalier F., Frangeul L., Msadek T., Zouine M., Couve E., Lalioui L., Poyart C., Trieu-Cuot P., Kunst F.
      Mol. Microbiol. 45:1499-1513(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: NEM316.
    2. "Substrate specificity of streptococcal unsaturated glucuronyl hydrolases for sulfated glycosaminoglycan."
      Maruyama Y., Nakamichi Y., Itoh T., Mikami B., Hashimoto W., Murata K.
      J. Biol. Chem. 284:18059-18069(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, ACTIVE SITE, INDUCTION, MUTAGENESIS OF ASP-115; ASP-175 AND ARG-236.
      Strain: NEM316.
    3. "Structural determinants in streptococcal unsaturated glucuronyl hydrolase for recognition of glycosaminoglycan sulfate groups."
      Nakamichi Y., Maruyama Y., Mikami B., Hashimoto W., Murata K.
      J. Biol. Chem. 286:6262-6271(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF WILD-TYPE AND MUTANT ASN-155 IN COMPLEX WITH N-ACETYL-D-GALACTOSAMINE 6-SULFATE, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF SER-365; SER-368 AND LYS-370.
      Strain: NEM316.
    4. "Crystal structure of unsaturated glucuronyl hydrolase mutant D115N from Streptcoccus agalactiae."
      Nakamichi Y., Maruyama Y., Mikami B., Hashimoto W., Murata K.
      Submitted (SEP-2012) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF MUTANT ASN-155.
      Strain: NEM316.

    Entry informationi

    Entry nameiUCDH_STRA3
    AccessioniPrimary (citable) accession number: Q8E372
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 3, 2013
    Last sequence update: March 1, 2003
    Last modified: February 17, 2016
    This is version 68 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Ser-365 and Ser-368 bind the sulfated group in the substrate and determine the preference for sulfated glycosaminoglycans compared to unsulfated glycosaminoglycans.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome

    Documents

    1. Glycosyl hydrolases
      Classification of glycosyl hydrolase families and list of entries
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.