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Protein

Alginate lyase

Gene

algL

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the depolymerization of alginate by cleaving the beta-1,4 glycosidic bond between two adjacent sugar residues via a beta-elimination mechanism (PubMed:8370530, PubMed:8335634, PubMed:23215237). May serve to degrade mislocalized alginate that is trapped in the periplasmic space. Acts preferentially on non-acetylated alginate or its precursor mannuronan. Is able to catalyze cleavage adjacent to either mannuronate or guluronate residues in alginate. Exhaustive digestion of alginate by AlgL generates dimeric and trimeric products (PubMed:23215237). In addition to its enzymatic function, AlgL appears to be required for alginate export, maybe as part of a multi-protein alginate-secretion complex (PubMed:16177314).4 Publications

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.UniRule annotation1 Publication

Kineticsi

kcat is 32 sec(-1) for the depolymerization of mannuronan (dp value of 133). kcat is 1.5 sec(-1) for the depolymerization of acetylated mannuronan (dp value of 133). kcat is 32 sec(-1) for the depolymerization of alginate (dp value of 263). kcat is 1.2 sec(-1) for the depolymerization of acetylated alginate (dp value of 263). The catalytic efficiency of the depolymerization reaction increases linearly with the number of residues in the substrate.1 Publication

  1. KM=13 µM for mannuronan (dp value of 133)1 Publication
  2. KM=5 µM for acetylated mannuronan (dp value of 133)1 Publication
  3. KM=13 µM for alginate (dp value of 263)1 Publication
  4. KM=2.6 µM for acetylated alginate (dp value of 263)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei256 – 2561SubstrateCombined sources1 Publication

    GO - Molecular functioni

    • L-threonine ammonia-lyase activity Source: PseudoCAP
    • poly(beta-D-mannuronate) lyase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    • alginic acid biosynthetic process Source: PseudoCAP
    • alginic acid catabolic process Source: PseudoCAP
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Enzyme and pathway databases

    BRENDAi4.2.2.3. 5087.

    Protein family/group databases

    CAZyiPL5. Polysaccharide Lyase Family 5.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Alginate lyase2 PublicationsUniRule annotation (EC:4.2.2.3UniRule annotation1 Publication)
    Alternative name(s):
    Poly(beta-D-mannuronate) lyaseUniRule annotation
    Gene namesi
    Name:algL2 PublicationsUniRule annotation
    Ordered Locus Names:PA3547
    OrganismiPseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
    Taxonomic identifieri208964 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
    Proteomesi
    • UP000002438 Componenti: Chromosome

    Organism-specific databases

    PseudoCAPiPA3547.

    Subcellular locationi

    • Periplasm UniRule annotation1 Publication1 Publication

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Periplasm

    Pathology & Biotechi

    Disruption phenotypei

    Deletion of algL is lethal, and microscopic examination of the cells reveals that alginate or a precursor accumulates in the periplasmic space until the cells burst.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 27271 PublicationAdd
    BLAST
    Chaini28 – 367340Alginate lyasePRO_0000024918Add
    BLAST

    Proteomic databases

    PaxDbiQ06749.

    Expressioni

    Inductioni

    Its expression is under the control of AlgB, which also regulates the alginate biosynthetic gene cluster.1 Publication

    Interactioni

    Protein-protein interaction databases

    STRINGi208964.PA3547.

    Structurei

    Secondary structure

    1
    367
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi34 – 374Combined sources
    Turni66 – 694Combined sources
    Helixi79 – 8810Combined sources
    Helixi90 – 10920Combined sources
    Helixi112 – 12817Combined sources
    Turni129 – 1313Combined sources
    Helixi138 – 16023Combined sources
    Helixi165 – 1684Combined sources
    Helixi170 – 19122Combined sources
    Helixi196 – 1983Combined sources
    Helixi201 – 21717Combined sources
    Helixi220 – 23617Combined sources
    Helixi244 – 2474Combined sources
    Helixi248 – 2525Combined sources
    Helixi253 – 27321Combined sources
    Helixi281 – 29818Combined sources
    Helixi301 – 3077Combined sources
    Helixi314 – 3174Combined sources
    Helixi319 – 3246Combined sources
    Helixi325 – 3317Combined sources
    Helixi336 – 34510Combined sources
    Helixi351 – 3533Combined sources
    Helixi357 – 3604Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4OZVX-ray1.64A28-362[»]
    4OZWX-ray1.64A28-362[»]
    ProteinModelPortaliQ06749.
    SMRiQ06749. Positions 28-362.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni65 – 662Substrate bindingCombined sources1 Publication
    Regioni138 – 1392Substrate bindingCombined sources1 Publication

    Sequence similaritiesi

    Belongs to the polysaccharide lyase 5 family.UniRule annotation

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiENOG4105FN4. Bacteria.
    ENOG4111N6J. LUCA.
    HOGENOMiHOG000247392.
    InParanoidiQ06749.
    KOiK01729.
    OMAiAAWSVMA.
    OrthoDBiEOG6H1PXF.

    Family and domain databases

    Gene3Di1.50.10.110. 1 hit.
    HAMAPiMF_00557. Alginate_lyase.
    InterProiIPR022859. Alginate_lyase.
    IPR008397. Alginate_lyase_dom.
    IPR008929. Chondroitin_lyas.
    [Graphical view]
    PfamiPF05426. Alginate_lyase. 1 hit.
    [Graphical view]
    SUPFAMiSSF48230. SSF48230. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    Q06749-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKTSHLIRIA LPGALAAALL ASQVSQAADL VPPPGYYAAV GERKGSAGSC
    60 70 80 90 100
    PAVPPPYTGS LVFTSKYEGS DSARATLNVK AEKTFRSQIK DITDMERGAT
    110 120 130 140 150
    KLVTQYMRSG RDGDLACALN WMSAWARAGA LQSDDFNHTG KSMRKWALGS
    160 170 180 190 200
    LSGAYMRLKF SSSRPLAAHA EQSREIEDWF ARLGTQVVRD WSGLPLKKIN
    210 220 230 240 250
    NHSYWAAWSV MSTAVVTNRR DLFDWAVSEF KVAANQVDEQ GFLPNELKRR
    260 270 280 290 300
    QRALAYHNYA LPPLAMIAAF AQVNGVDLRQ ENHGALQRLA ERVMKGVDDE
    310 320 330 340 350
    ETFEEKTGED QDMTDLKVDN KYAWLEPYCA LYRCEPKMLE AKKDREPFNS
    360
    FRLGGEVTRV FSREGGS
    Length:367
    Mass (Da):40,829
    Last modified:December 15, 1998 - v2
    Checksum:iEAA3FE30032AB3BA
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti269 – 2691A → P in AAA71990 (PubMed:8370530).Curated
    Sequence conflicti337 – 3415KMLEA → NACSRP in AAA71990 (PubMed:8370530).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L14597 Unassigned DNA. Translation: AAA71990.1.
    U27829 Genomic DNA. Translation: AAA91127.1.
    AE004091 Genomic DNA. Translation: AAG06935.1.
    PIRiH83202.
    JN0777.
    RefSeqiNP_252237.1. NC_002516.2.
    WP_003092108.1. NZ_ASJY01000573.1.

    Genome annotation databases

    EnsemblBacteriaiAAG06935; AAG06935; PA3547.
    GeneIDi878552.
    KEGGipae:PA3547.
    PATRICi19841707. VBIPseAer58763_3711.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L14597 Unassigned DNA. Translation: AAA71990.1.
    U27829 Genomic DNA. Translation: AAA91127.1.
    AE004091 Genomic DNA. Translation: AAG06935.1.
    PIRiH83202.
    JN0777.
    RefSeqiNP_252237.1. NC_002516.2.
    WP_003092108.1. NZ_ASJY01000573.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4OZVX-ray1.64A28-362[»]
    4OZWX-ray1.64A28-362[»]
    ProteinModelPortaliQ06749.
    SMRiQ06749. Positions 28-362.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi208964.PA3547.

    Protein family/group databases

    CAZyiPL5. Polysaccharide Lyase Family 5.

    Proteomic databases

    PaxDbiQ06749.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAG06935; AAG06935; PA3547.
    GeneIDi878552.
    KEGGipae:PA3547.
    PATRICi19841707. VBIPseAer58763_3711.

    Organism-specific databases

    PseudoCAPiPA3547.

    Phylogenomic databases

    eggNOGiENOG4105FN4. Bacteria.
    ENOG4111N6J. LUCA.
    HOGENOMiHOG000247392.
    InParanoidiQ06749.
    KOiK01729.
    OMAiAAWSVMA.
    OrthoDBiEOG6H1PXF.

    Enzyme and pathway databases

    BRENDAi4.2.2.3. 5087.

    Family and domain databases

    Gene3Di1.50.10.110. 1 hit.
    HAMAPiMF_00557. Alginate_lyase.
    InterProiIPR022859. Alginate_lyase.
    IPR008397. Alginate_lyase_dom.
    IPR008929. Chondroitin_lyas.
    [Graphical view]
    PfamiPF05426. Alginate_lyase. 1 hit.
    [Graphical view]
    SUPFAMiSSF48230. SSF48230. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Sequence of the algL gene of Pseudomonas aeruginosa and purification of its alginate lyase product."
      Boyd A., Ghosh M., May T.B., Shinabarger D., Keogh R., Chakrabarty A.M.
      Gene 131:1-8(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, SUBCELLULAR LOCATION.
      Strain: 8830.
    2. "Characterization of the Pseudomonas aeruginosa alginate lyase gene (algL): cloning, sequencing, and expression in Escherichia coli."
      Schiller N.L., Monday S.R., Boyd C.M., Keen N.T., Ohman D.E.
      J. Bacteriol. 175:4780-4789(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 28-43, FUNCTION, INDUCTION, SUBCELLULAR LOCATION.
      Strain: FRD1.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
    4. "Role of an alginate lyase for alginate transport in mucoid Pseudomonas aeruginosa."
      Jain S., Ohman D.E.
      Infect. Immun. 73:6429-6436(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
      Strain: FRD1.
    5. "Functional characterization of AlgL, an alginate lyase from Pseudomonas aeruginosa."
      Farrell E.K., Tipton P.A.
      Biochemistry 51:10259-10266(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
    6. "Crystal structure of the periplasmic alginate lyase AlgL and the AlgL H202A mutant."
      Howell P.L., Wolfram F., Robinson H., Arora K.
      Submitted (FEB-2014) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.64 ANGSTROMS) OF 28-362 OF WILD-TYPE AND MUTANT ALA-202 IN COMPLEX WITH BETA-D-MANNURONATE.
      Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.

    Entry informationi

    Entry nameiALGL_PSEAE
    AccessioniPrimary (citable) accession number: Q06749
    Secondary accession number(s): Q57292
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: December 15, 1998
    Last modified: May 11, 2016
    This is version 103 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.