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Protein

Beta-agarase B

Gene

agaB

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. Also tolerant to hybrid substrates containing C6-sulfate groups at the -4, +1, and +3 positions.2 Publications

Catalytic activityi

Hydrolysis of (1->4)-beta-D-galactosidic linkages in agarose, giving the tetramer as the predominant product.2 Publications

Kineticsi

kcat is 100 sec(-1).

  1. KM=1 mM for agarose1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei181 – 1811Substrate1 Publication
    Active sitei184 – 1841NucleophileBy similarity
    Active sitei189 – 1891Proton donorBy similarity
    Binding sitei215 – 2151Substrate1 Publication
    Binding sitei219 – 2191Substrate1 Publication
    Binding sitei224 – 2241Substrate1 Publication
    Binding sitei226 – 2261Substrate1 Publication
    Binding sitei308 – 3081Substrate1 Publication

    GO - Molecular functioni

    • beta-agarase activity Source: UniProtKB
    • protein homodimerization 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

    BioCyciMetaCyc:MONOMER-16650.
    ZGAL63186:GJN9-3573-MONOMER.
    BRENDAi3.2.1.81. 7557.

    Protein family/group databases

    CAZyiGH16. Glycoside Hydrolase Family 16.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Beta-agarase B (EC:3.2.1.81)
    Gene namesi
    Name:agaB
    Ordered Locus Names:zobellia_3573
    OrganismiZobellia galactanivorans (strain DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij)
    Taxonomic identifieri63186 [NCBI]
    Taxonomic lineageiBacteriaBacteroidetesFlavobacteriiaFlavobacterialesFlavobacteriaceaeZobellia
    Proteomesi
    • UP000008898 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    • cell outer membrane Source: UniProtKB
    Complete GO annotation...

    Keywords - Cellular componenti

    Cell outer membrane, Membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi189 – 1891E → D: Abolishes beta-agarase activity.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 1717PROSITE-ProRule annotationAdd
    BLAST
    Chaini18 – 353336Beta-agarase BPRO_5000055270Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi18 – 181N-palmitoyl cysteinePROSITE-ProRule annotation
    Lipidationi18 – 181S-diacylglycerol cysteinePROSITE-ProRule annotation

    Keywords - PTMi

    Lipoprotein, Palmitate

    Expressioni

    Inductioni

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

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    GO - Molecular functioni

    • protein homodimerization activity Source: UniProtKB

    Structurei

    Secondary structure

    1
    353
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi60 – 623Combined sources
    Beta strandi73 – 775Combined sources
    Helixi95 – 1006Combined sources
    Beta strandi101 – 1044Combined sources
    Beta strandi106 – 1083Combined sources
    Beta strandi115 – 1173Combined sources
    Helixi119 – 1213Combined sources
    Beta strandi122 – 1254Combined sources
    Beta strandi128 – 1325Combined sources
    Beta strandi142 – 1443Combined sources
    Beta strandi146 – 1516Combined sources
    Beta strandi155 – 16410Combined sources
    Beta strandi167 – 17812Combined sources
    Beta strandi181 – 19111Combined sources
    Beta strandi194 – 1963Combined sources
    Turni197 – 2004Combined sources
    Helixi204 – 2074Combined sources
    Beta strandi214 – 2185Combined sources
    Turni219 – 2224Combined sources
    Beta strandi223 – 2253Combined sources
    Helixi230 – 2323Combined sources
    Helixi240 – 2423Combined sources
    Beta strandi245 – 2539Combined sources
    Beta strandi256 – 2616Combined sources
    Beta strandi264 – 2718Combined sources
    Helixi272 – 2754Combined sources
    Beta strandi282 – 2854Combined sources
    Beta strandi301 – 3088Combined sources
    Helixi311 – 3144Combined sources
    Helixi321 – 3233Combined sources
    Helixi329 – 3324Combined sources
    Helixi336 – 3383Combined sources
    Beta strandi339 – 35214Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1O4ZX-ray2.30A/B/C/D19-353[»]
    4ATFX-ray1.90A/B/C/D53-353[»]
    ProteinModelPortaliQ9RGX8.
    SMRiQ9RGX8. Positions 58-353.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9RGX8.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini58 – 353296GH16PROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni105 – 1073Substrate 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.
    OMAiLASDVWL.

    Family and domain databases

    Gene3Di2.60.120.200. 1 hit.
    InterProiIPR016287. Agarase.
    IPR013320. ConA-like_dom.
    IPR000757. GH16.
    [Graphical view]
    PfamiPF00722. Glyco_hydro_16. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001097. Agarase. 1 hit.
    SUPFAMiSSF49899. SSF49899. 1 hit.
    PROSITEiPS51762. GH16_2. 1 hit.
    PS51257. PROKAR_LIPOPROTEIN. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q9RGX8-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MYLIYLRLVF CCALLLGCGD NSKFDSATDL PVEQEQEQET EQEGEPEESS
    60 70 80 90 100
    EQDLVEEVDW KDIPVPADAG PNMKWEFQEI SDNFEYEAPA DNKGSEFLEK
    110 120 130 140 150
    WDDFYHNAWA GPGLTEWKRD RSYVADGELK MWATRKPGSD KINMGCITSK
    160 170 180 190 200
    TRVVYPVYIE ARAKVMNSTL ASDVWLLSAD DTQEIDILEA YGADYSESAG
    210 220 230 240 250
    KDHSYFSKKV HISHHVFIRD PFQDYQPKDA GSWFEDGTVW NKEFHRFGVY
    260 270 280 290 300
    WRDPWHLEYY IDGVLVRTVS GKDIIDPKHF TNTTDPGNTE IDTRTGLNKE
    310 320 330 340 350
    MDIIINTEDQ TWRSSPASGL QSNTYTPTDN ELSNIENNTF GVDWIRIYKP

    VEK
    Length:353
    Mass (Da):40,675
    Last modified:May 1, 2000 - v1
    Checksum:i2281286B0F30F9FC
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF098955 Genomic DNA. Translation: AAF21821.1.
    FP476056 Genomic DNA. Translation: CAZ97711.1.
    RefSeqiWP_013994901.1. NC_015844.1.

    Genome annotation databases

    EnsemblBacteriaiCAZ97711; CAZ97711; ZOBELLIA_3573.
    KEGGizga:ZOBELLIA_3573.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF098955 Genomic DNA. Translation: AAF21821.1.
    FP476056 Genomic DNA. Translation: CAZ97711.1.
    RefSeqiWP_013994901.1. NC_015844.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1O4ZX-ray2.30A/B/C/D19-353[»]
    4ATFX-ray1.90A/B/C/D53-353[»]
    ProteinModelPortaliQ9RGX8.
    SMRiQ9RGX8. Positions 58-353.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein family/group databases

    CAZyiGH16. Glycoside Hydrolase Family 16.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAZ97711; CAZ97711; ZOBELLIA_3573.
    KEGGizga:ZOBELLIA_3573.

    Phylogenomic databases

    KOiK01219.
    OMAiLASDVWL.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16650.
    ZGAL63186:GJN9-3573-MONOMER.
    BRENDAi3.2.1.81. 7557.

    Miscellaneous databases

    EvolutionaryTraceiQ9RGX8.

    Family and domain databases

    Gene3Di2.60.120.200. 1 hit.
    InterProiIPR016287. Agarase.
    IPR013320. ConA-like_dom.
    IPR000757. GH16.
    [Graphical view]
    PfamiPF00722. Glyco_hydro_16. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001097. Agarase. 1 hit.
    SUPFAMiSSF49899. SSF49899. 1 hit.
    PROSITEiPS51762. GH16_2. 1 hit.
    PS51257. PROKAR_LIPOPROTEIN. 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], 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. Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 19-353.
    4. "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: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 53-353 OF MUTANT ASP-189 IN COMPLEX WITH NEOAGAROOCTAOSE, FUNCTION, CATALYTIC ACTIVITY, INDUCTION.

    Entry informationi

    Entry nameiAGAB_ZOBGA
    AccessioniPrimary (citable) accession number: Q9RGX8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 3, 2013
    Last sequence update: May 1, 2000
    Last modified: March 16, 2016
    This is version 78 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, 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.