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Protein

Beta-agarase A

Gene

agaA

Organism
Zobellia galactanivorans (strain DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Cleaves the beta-1,4-linkages between beta-D-galactose and alpha-L-3,6-anhydro-galactose residues in agarose. Cleaves agarose in a random manner with retention of the anomeric-bond configuration, producing beta-anomers that give rise progressively to alpha-anomers when mutarotation takes place.1 Publication

Catalytic activityi

Hydrolysis of (1->4)-beta-D-galactosidic linkages in agarose, giving the tetramer as the predominant product.1 Publication

Kineticsi

kcat is 150 sec(-1).

  1. KM=2 mM for agarose1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei73 – 731Substrate1 Publication
    Binding sitei144 – 1441Substrate1 Publication
    Active sitei147 – 1471Nucleophile1 Publication
    Active sitei152 – 1521Proton donor1 Publication
    Binding sitei176 – 1761Substrate1 Publication
    Binding sitei271 – 2711Substrate1 Publication

    GO - Molecular functioni

    • beta-agarase activity Source: UniProtKB

    GO - Biological processi

    • carbohydrate metabolic process Source: UniProtKB
    • metabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Enzyme and pathway databases

    BioCyciZGAL63186:GJN9-4203-MONOMER.
    BRENDAi3.2.1.81. 7557.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Beta-agarase A (EC:3.2.1.81)
    Cleaved into the following chain:
    Gene namesi
    Name:agaA
    Ordered Locus Names:zobellia_4203
    OrganismiZobellia galactanivorans (strain DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij)
    Taxonomic identifieri63186 [NCBI]
    Taxonomic lineageiBacteriaBacteroidetesFlavobacteriiaFlavobacterialesFlavobacteriaceaeZobellia
    Proteomesi
    • UP000008898 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    • extracellular region Source: UniProtKB
    Complete GO annotation...

    Keywords - Cellular componenti

    Secreted

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi147 – 1471E → S: Abolishes beta-agarase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 1919Sequence analysisAdd
    BLAST
    Chaini20 – 539520Beta-agarase APRO_5000055268Add
    BLAST
    Chaini20 – 295276Beta-agarase A catalytic chainPRO_5000055269Add
    BLAST

    Post-translational modificationi

    Proteolytically cleaved into mature beta-agarase A catalytic chain (AgaAc).1 Publication

    Expressioni

    Inductioni

    When cells are grown with the low sulfated agar.1 Publication

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Structurei

    Secondary structure

    1
    539
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni22 – 254Combined sources
    Beta strandi36 – 405Combined sources
    Helixi42 – 443Combined sources
    Beta strandi50 – 534Combined sources
    Helixi59 – 624Combined sources
    Beta strandi65 – 684Combined sources
    Beta strandi70 – 723Combined sources
    Beta strandi79 – 813Combined sources
    Helixi83 – 853Combined sources
    Beta strandi86 – 916Combined sources
    Beta strandi93 – 1019Combined sources
    Beta strandi104 – 1074Combined sources
    Beta strandi109 – 1146Combined sources
    Beta strandi118 – 12710Combined sources
    Beta strandi130 – 14011Combined sources
    Beta strandi146 – 1549Combined sources
    Helixi157 – 1593Combined sources
    Helixi161 – 1644Combined sources
    Beta strandi166 – 17510Combined sources
    Turni176 – 1794Combined sources
    Beta strandi180 – 1823Combined sources
    Helixi187 – 1893Combined sources
    Beta strandi190 – 1923Combined sources
    Helixi198 – 2003Combined sources
    Beta strandi203 – 2119Combined sources
    Beta strandi214 – 2196Combined sources
    Beta strandi222 – 2276Combined sources
    Helixi229 – 2324Combined sources
    Turni237 – 2404Combined sources
    Beta strandi247 – 2548Combined sources
    Turni257 – 2593Combined sources
    Helixi265 – 2695Combined sources
    Turni271 – 2733Combined sources
    Beta strandi274 – 28815Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1O4YX-ray1.48A20-295[»]
    1URXX-ray1.70A20-290[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini21 – 289269GH16PROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni82 – 9211Substrate binding1 PublicationAdd
    BLAST
    Regioni96 – 983Substrate binding1 Publication

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 16 family.Curated
    Contains 1 GH16 (glycosyl hydrolase family 16) domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Signal

    Phylogenomic databases

    KOiK01219.

    Family and domain databases

    Gene3Di2.60.120.200. 1 hit.
    InterProiIPR013320. ConA-like_dom.
    IPR008979. Galactose-bd-like.
    IPR000757. GH16.
    IPR026444. Secre_tail.
    [Graphical view]
    SUPFAMiSSF49785. SSF49785. 1 hit.
    SSF49899. SSF49899. 1 hit.
    TIGRFAMsiTIGR04183. Por_Secre_tail. 1 hit.
    PROSITEiPS51762. GH16_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    G0L322-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKKNYLLLYF IFLLCGSIAA QDWNGIPVPA NPGNGMTWQL QDNVSDSFNY
    60 70 80 90 100
    TSSEGNRPTA FTSKWKPSYI NGWTGPGSTI FNAPQAWTNG SQLAIQAQPA
    110 120 130 140 150
    GNGKSYNGII TSKNKIQYPV YMEIKAKIMD QVLANAFWTL TDDETQEIDI
    160 170 180 190 200
    MEGYGSDRGG TWFAQRMHLS HHTFIRNPFT DYQPMGDATW YYNGGTPWRS
    210 220 230 240 250
    AYHRYGCYWK DPFTLEYYID GVKVRTVTRA EIDPNNHLGG TGLNQATNII
    260 270 280 290 300
    IDCENQTDWR PAATQEELAD DSKNIFWVDW IRVYKPVAVS GGGNNGNDGA
    310 320 330 340 350
    TEFQYDLGTD TSAVWPGYTR VSNTTRAGNF GWANTNDIGS RDRGASNGRN
    360 370 380 390 400
    NINRDINFSS QTRFFTQDLS NGTYNVLITF GDTYARKNMN VAAEGQNKLT
    410 420 430 440 450
    NINTNAGQYV SRSFDVNVND GKLDLRFSVG NGGDVWSITR IWIRKVTSNS
    460 470 480 490 500
    ANLLAAKGLT LEDPVETTEF LYPNPAKTDD FVTVPNSEIG SSIIIYNSAG
    510 520 530
    QVVKKVSVVS ENQKISLEGF AKGMYFINLN GQSTKLIVQ
    Length:539
    Mass (Da):60,020
    Last modified:October 19, 2011 - v1
    Checksum:i8D60A87DBF009A44
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti84 – 841P → A in AAF21820 (PubMed:15456406).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF098954 Genomic DNA. Translation: AAF21820.1.
    FP476056 Genomic DNA. Translation: CAZ98338.1.

    Genome annotation databases

    EnsemblBacteriaiCAZ98338; CAZ98338; ZOBELLIA_4203.
    KEGGizga:ZOBELLIA_4203.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF098954 Genomic DNA. Translation: AAF21820.1.
    FP476056 Genomic DNA. Translation: CAZ98338.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1O4YX-ray1.48A20-295[»]
    1URXX-ray1.70A20-290[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAZ98338; CAZ98338; ZOBELLIA_4203.
    KEGGizga:ZOBELLIA_4203.

    Phylogenomic databases

    KOiK01219.

    Enzyme and pathway databases

    BioCyciZGAL63186:GJN9-4203-MONOMER.
    BRENDAi3.2.1.81. 7557.

    Family and domain databases

    Gene3Di2.60.120.200. 1 hit.
    InterProiIPR013320. ConA-like_dom.
    IPR008979. Galactose-bd-like.
    IPR000757. GH16.
    IPR026444. Secre_tail.
    [Graphical view]
    SUPFAMiSSF49785. SSF49785. 1 hit.
    SSF49899. SSF49899. 1 hit.
    TIGRFAMsiTIGR04183. Por_Secre_tail. 1 hit.
    PROSITEiPS51762. GH16_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "The endo-beta-agarases AgaA and AgaB from the marine bacterium Zobellia galactanivorans: two paralogue enzymes with different molecular organizations and catalytic behaviours."
      Jam M., Flament D., Allouch J., Potin P., Thion L., Kloareg B., Czjzek M., Helbert W., Michel G., Barbeyron T.
      Biochem. J. 385:703-713(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 116-125, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, SUBCELLULAR LOCATION.
      Strain: DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij.
    2. "Complete genome sequence of Zobellia galactanivorans Dsij."
      Genoscope - CEA
      Submitted (JUL-2009) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij.
    3. "Biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium Zobellia galactanivorans."
      Hehemann J.H., Correc G., Thomas F., Bernard T., Barbeyron T., Jam M., Helbert W., Michel G., Czjzek M.
      J. Biol. Chem. 287:30571-30584(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
      Strain: DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij.
    4. Cited for: X-RAY CRYSTALLOGRAPHY (1.48 ANGSTROMS) OF 20-295, ACTIVE SITE.
      Strain: DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij.
    5. "Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose."
      Allouch J., Helbert W., Henrissat B., Czjzek M.
      Structure 12:623-632(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 20-290 OF MUTANT SER-147 IN COMPLEX WITH GALACTOSE, MUTAGENESIS OF GLU-147.
      Strain: DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij.

    Entry informationi

    Entry nameiAGAA_ZOBGA
    AccessioniPrimary (citable) accession number: G0L322
    Secondary accession number(s): Q9RGX9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 3, 2013
    Last sequence update: October 19, 2011
    Last modified: March 16, 2016
    This is version 30 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

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