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Protein

Alginate lyase

Gene

algL

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
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

Manual assertion based on experiment ini

  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)DescriptionActionsGraphical viewLength
    Binding sitei256SubstrateCombined sources1 Publication1

    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 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
    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)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 271 PublicationAdd BLAST27
    ChainiPRO_000002491828 – 367Alginate lyaseAdd BLAST340

    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

    1367
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi34 – 37Combined sources4
    Turni66 – 69Combined sources4
    Helixi79 – 88Combined sources10
    Helixi90 – 109Combined sources20
    Helixi112 – 128Combined sources17
    Turni129 – 131Combined sources3
    Helixi138 – 160Combined sources23
    Helixi165 – 168Combined sources4
    Helixi170 – 191Combined sources22
    Helixi196 – 198Combined sources3
    Helixi201 – 217Combined sources17
    Helixi220 – 236Combined sources17
    Helixi244 – 247Combined sources4
    Helixi248 – 252Combined sources5
    Helixi253 – 273Combined sources21
    Helixi281 – 298Combined sources18
    Helixi301 – 307Combined sources7
    Helixi314 – 317Combined sources4
    Helixi319 – 324Combined sources6
    Helixi325 – 331Combined sources7
    Helixi336 – 345Combined sources10
    Helixi351 – 353Combined sources3
    Helixi357 – 360Combined sources4

    3D structure databases

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

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni65 – 66Substrate bindingCombined sources1 Publication2
    Regioni138 – 139Substrate bindingCombined sources1 Publication2

    Sequence similaritiesi

    Belongs to the polysaccharide lyase 5 family.UniRule annotation

    Keywords - Domaini

    Signal

    Phylogenomic databases

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

    Family and domain databases

    CDDicd00244. AlgLyase. 1 hit.
    Gene3Di1.50.10.110. 1 hit.
    HAMAPiMF_00557. Alginate_lyase. 1 hit.
    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)DescriptionActionsGraphical viewLength
    Sequence conflicti269A → P in AAA71990 (PubMed:8370530).Curated1
    Sequence conflicti337 – 341KMLEA → NACSRP in AAA71990 (PubMed:8370530).Curated5

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4OZVX-ray1.64A28-362[»]
    4OZWX-ray1.64A28-362[»]
    ProteinModelPortaliQ06749.
    SMRiQ06749.
    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.

    Enzyme and pathway databases

    BRENDAi4.2.2.3. 5087.

    Family and domain databases

    CDDicd00244. AlgLyase. 1 hit.
    Gene3Di1.50.10.110. 1 hit.
    HAMAPiMF_00557. Alginate_lyase. 1 hit.
    InterProiIPR022859. Alginate_lyase.
    IPR008397. Alginate_lyase_dom.
    IPR008929. Chondroitin_lyas.
    [Graphical view]
    PfamiPF05426. Alginate_lyase. 1 hit.
    [Graphical view]
    SUPFAMiSSF48230. SSF48230. 1 hit.
    ProtoNetiSearch...

    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: November 2, 2016
    This is version 106 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.