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Protein

Polysaccharide lyase

Gene

Smlt1473

Organism
Stenotrophomonas maltophilia (strain K279a)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Polysaccharide lyase that catalyzes the depolymerization of several anionic polysaccharides via a beta-elimination mechanism. Exhibits broad substrate specificity, catalyzing the degradation of not only alginate and poly-beta-D-mannuronate (poly-ManA), but poly-beta-D-glucuronate (poly-GlcA or poly-GlcUA) and hyaluronate (HA) as well. The oligosaccharide products formed by enzymatic cleavage are comprised mainly of disaccharides, with a lower abundance of trimers and pentamers. Is not active on poly-D-galacturonate, heparin and heparin sulfate.1 Publication

Catalytic activityi

Eliminative cleavage of alginate to give oligosaccharides with 4-deoxy-alpha-L-erythro-hex-4-enuronosyl groups at their non-reducing ends and beta-D-mannuronate at their reducing end.1 Publication
Cleaves hyaluronate chains at a beta-D-GlcNAc-(1->4)-beta-D-GlcA bond, ultimately breaking the polysaccharide down to 3-(4-deoxy-beta-D-gluc-4-enuronosyl)-N-acetyl-D-glucosamine.1 Publication
Eliminative cleavage of (1->4)-beta-D-glucuronans to give oligosaccharides with 4-deoxy-beta-D-gluc-4-enuronosyl groups at their non-reducing ends. Complete degradation of glucuronans results in the formation of tetrasaccharides.1 Publication

Enzyme regulationi

Is inhibited by mono- and divalent cations as well as L-ascorbic acid 6-hexadecanoate.1 Publication

Kineticsi

Vmax for poly-GlcA is about 10-fold greater versus poly-ManA or HA (PubMed:24257754). kcat is 31.9 sec(-1) with poly-GlcA as substrate (at pH 7) (PubMed:24808176). kcat is 3.3 sec(-1) with poly-ManA as substrate (at pH 9) (PubMed:24808176).2 Publications

  1. KM=0.14 mg/ml for poly-GlcA1 Publication
  2. KM=0.26 mg/ml for poly-ManA1 Publication
  3. KM=0.55 mg/ml for hyaluronan1 Publication
  4. KM=0.17 mM for poly-GlcA (at pH 7)1 Publication
  5. KM=0.35 mM for poly-ManA (at pH 9)1 Publication

    pH dependencei

    Optimum pH for enzymatic activity is substrate-dependent, with optimal hyaluronate degradation at pH 5, poly-beta-D-glucuronate degradation at pH 7, and alginate degradation at pH 9.1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Carbohydrate metabolism, Polysaccharide degradation

    Enzyme and pathway databases

    BioCyciSMAL522373:GJE8-1431-MONOMER.

    Protein family/group databases

    CAZyiPL5. Polysaccharide Lyase Family 5.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Polysaccharide lyase1 Publication (EC:4.2.2.-1 Publication)
    Short name:
    PL1 Publication
    Alternative name(s):
    Alginate lyase1 Publication (EC:4.2.2.31 Publication)
    Endolytic polysaccharide lyaseCurated
    Hyaluronate lyase1 Publication (EC:4.2.2.11 Publication)
    Multifunctional polysaccharide lyase1 Publication
    Poly-beta-D-glucuronate lyase1 Publication (EC:4.2.2.141 Publication)
    Gene namesi
    Ordered Locus Names:Smlt1473
    OrganismiStenotrophomonas maltophilia (strain K279a)
    Taxonomic identifieri522373 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeStenotrophomonasStenotrophomonas maltophilia group
    Proteomesi
    • UP000008840 Componenti: Chromosome

    Subcellular locationi

    • Cell outer membrane 1 Publication; Lipid-anchor PROSITE-ProRule annotation1 Publication

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cell outer membrane, Membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi23 – 231C → F: Impairs subcellular location since the protein mutant is completely retained in the cytosol. Loss of extracellular lyase activity in mutant cells. 1 Publication
    Mutagenesisi167 – 1671N → L: Less than 0.5% of wild-type activity against all substrates. 1 Publication
    Mutagenesisi168 – 1681H → A: Retains 10% of activity toward poly-GlcA, but shows less than 0.5% of wild-type activity against poly-ManA and HA. 1 Publication
    Mutagenesisi171 – 1711W → A: Displays nearly eliminated HA activity, while increasing poly-ManA and poly-GlcA activity by at least 35%. 1 Publication
    Mutagenesisi215 – 2151R → L: Less than 0.5% of wild-type activity against all substrates. 1 Publication
    Mutagenesisi221 – 2211H → F: Increases activity and specificity toward poly-ManA. 1 Publication
    Mutagenesisi222 – 2221Y → F: Less than 0.5% of wild-type activity against all substrates. 1 Publication
    Mutagenesisi312 – 3121R → L: Increases activity and specificity toward poly-GlcA. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2222CuratedAdd
    BLAST
    Chaini23 – 331309Polysaccharide lyasePRO_5000341778Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi23 – 231N-palmitoyl cysteineCurated
    Lipidationi23 – 231S-diacylglycerol cysteineCurated

    Keywords - PTMi

    Lipoprotein, Palmitate

    Interactioni

    Protein-protein interaction databases

    STRINGi522373.Smlt1473.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polysaccharide lyase 5 family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiENOG4105FN4. Bacteria.
    ENOG4111N6J. LUCA.
    HOGENOMiHOG000056685.
    KOiK01729.
    OMAiAAWSVMA.
    OrthoDBiEOG6H1PXF.

    Family and domain databases

    Gene3Di1.50.10.110. 1 hit.
    InterProiIPR008397. Alginate_lyase_dom.
    IPR008929. Chondroitin_lyas.
    [Graphical view]
    PfamiPF05426. Alginate_lyase. 1 hit.
    [Graphical view]
    SUPFAMiSSF48230. SSF48230. 1 hit.
    PROSITEiPS51257. PROKAR_LIPOPROTEIN. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    B2FHL8-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSLPLRLALL PTLLASASAF AACPAPPPGQ PDIRAIGYYT DKAGSVIDPA
    60 70 80 90 100
    LQQQNKDATA PLDRYAADVA RMSDDYLRNG DPAAAQCTLS WLGAWADDGA
    110 120 130 140 150
    MLGQMIRVNN DQSFYMRQWM LDAVAMAYLK VHDQANPQQR ARIDPWLQKL
    160 170 180 190 200
    ARANLAYWDN PKRRRNNHYY WGGLGVLATG LATDDDALWQ AGHAAFQKGI
    210 220 230 240 250
    DDIQDDGSLP LEMARGQRAL HYHDYALAPL VMMAELARLR GQDWYASRNH
    260 270 280 290 300
    AIDRLARRVI EGSRDPAWFN QHTGAAQLPL QASGWVEFYR LRSPDGGVFD
    310 320 330
    AAHARGPFHS PRLGGDLTLM ATHGIVRTPL R
    Length:331
    Mass (Da):36,696
    Last modified:June 10, 2008 - v1
    Checksum:iB3D40DDFE2714589
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AM743169 Genomic DNA. Translation: CAQ45011.1.
    RefSeqiWP_012479599.1. NC_010943.1.

    Genome annotation databases

    EnsemblBacteriaiCAQ45011; CAQ45011; Smlt1473.
    GeneIDi6395630.
    KEGGisml:Smlt1473.
    PATRICi23698649. VBISteMal45202_1413.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AM743169 Genomic DNA. Translation: CAQ45011.1.
    RefSeqiWP_012479599.1. NC_010943.1.

    3D structure databases

    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi522373.Smlt1473.

    Protein family/group databases

    CAZyiPL5. Polysaccharide Lyase Family 5.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAQ45011; CAQ45011; Smlt1473.
    GeneIDi6395630.
    KEGGisml:Smlt1473.
    PATRICi23698649. VBISteMal45202_1413.

    Phylogenomic databases

    eggNOGiENOG4105FN4. Bacteria.
    ENOG4111N6J. LUCA.
    HOGENOMiHOG000056685.
    KOiK01729.
    OMAiAAWSVMA.
    OrthoDBiEOG6H1PXF.

    Enzyme and pathway databases

    BioCyciSMAL522373:GJE8-1431-MONOMER.

    Family and domain databases

    Gene3Di1.50.10.110. 1 hit.
    InterProiIPR008397. Alginate_lyase_dom.
    IPR008929. Chondroitin_lyas.
    [Graphical view]
    PfamiPF05426. Alginate_lyase. 1 hit.
    [Graphical view]
    SUPFAMiSSF48230. SSF48230. 1 hit.
    PROSITEiPS51257. PROKAR_LIPOPROTEIN. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants."
      Crossman L.C., Gould V.C., Dow J.M., Vernikos G.S., Okazaki A., Sebaihia M., Saunders D., Arrowsmith C., Carver T., Peters N., Adlem E., Kerhornou A., Lord A., Murphy L., Seeger K., Squares R., Rutter S., Quail M.A.
      , Rajandream M.A., Harris D., Churcher C., Bentley S.D., Parkhill J., Thomson N.R., Avison M.B.
      Genome Biol. 9:R74.1-R74.13(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K279a.
    2. "A polysaccharide lyase from Stenotrophomonas maltophilia with a unique, pH-regulated substrate specificity."
      MacDonald L.C., Berger B.W.
      J. Biol. Chem. 289:312-325(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBCELLULAR LOCATION, MUTAGENESIS OF CYS-23; ASN-167; HIS-168; ARG-215 AND TYR-222.
      Strain: K279a.
    3. "Insight into the role of substrate-binding residues in conferring substrate specificity for the multifunctional polysaccharide lyase Smlt1473."
      MacDonald L.C., Berger B.W.
      J. Biol. Chem. 289:18022-18032(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: 3D-STRUCTURE MODELING, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF TRP-171; HIS-221 AND ARG-312.
      Strain: K279a.

    Entry informationi

    Entry nameiPL_STRMK
    AccessioniPrimary (citable) accession number: B2FHL8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 9, 2014
    Last sequence update: June 10, 2008
    Last modified: May 11, 2016
    This is version 45 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. 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.