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Protein

Beta-agarase B

Gene

agaB

Organism
Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
    Binding sitei181Substrate1 Publication1
    Active sitei184NucleophileBy similarity1
    Active sitei189Proton donorBy similarity1
    Binding sitei215Substrate1 Publication1
    Binding sitei219Substrate1 Publication1
    Binding sitei224Substrate1 Publication1
    Binding sitei226Substrate1 Publication1
    Binding sitei308Substrate1 Publication1

    GO - Molecular functioni

    • beta-agarase activity Source: UniProtKB
    • protein homodimerization activity Source: UniProtKB

    GO - Biological processi

    Keywordsi

    Molecular functionGlycosidase, Hydrolase

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16650
    ZGAL63186:ZOBGAL_RS16795-MONOMER
    BRENDAi3.2.1.81 7557
    SABIO-RKiQ9RGX8

    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 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij)
    Taxonomic identifieri63186 [NCBI]
    Taxonomic lineageiBacteriaBacteroidetesFlavobacteriiaFlavobacterialesFlavobacteriaceaeZobellia
    Proteomesi
    • UP000008898 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    • cell outer membrane Source: UniProtKB

    Keywords - Cellular componenti

    Cell outer membrane, Membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi189E → D: Abolishes beta-agarase activity. 1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 17PROSITE-ProRule annotationAdd BLAST17
    ChainiPRO_500005527018 – 353Beta-agarase BAdd BLAST336

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Lipidationi18N-palmitoyl cysteinePROSITE-ProRule annotation1
    Lipidationi18S-diacylglycerol cysteinePROSITE-ProRule annotation1

    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

    Structurei

    Secondary structure

    1353
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliQ9RGX8
    SMRiQ9RGX8
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9RGX8

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini58 – 353GH16PROSITE-ProRule annotationAdd BLAST296

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni105 – 107Substrate binding1 Publication3

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 16 family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    KOiK01219
    OMAiLASDVWL

    Family and domain databases

    CDDicd02178 GH16_beta_agarase, 1 hit
    InterProiView protein in InterPro
    IPR016287 Beta_agarase
    IPR013320 ConA-like_dom_sf
    IPR000757 GH16
    PfamiView protein in Pfam
    PF00722 Glyco_hydro_16, 1 hit
    PIRSFiPIRSF001097 Agarase, 1 hit
    SUPFAMiSSF49899 SSF49899, 1 hit
    PROSITEiView protein in PROSITE
    PS51762 GH16_2, 1 hit
    PS51257 PROKAR_LIPOPROTEIN, 1 hit

    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
    PATRICifig|63186.3.peg.3487

    Similar proteinsi

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1O4ZX-ray2.30A/B/C/D19-353[»]
    4ATFX-ray1.90A/B/C/D53-353[»]
    ProteinModelPortaliQ9RGX8
    SMRiQ9RGX8
    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
    PATRICifig|63186.3.peg.3487

    Phylogenomic databases

    KOiK01219
    OMAiLASDVWL

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16650
    ZGAL63186:ZOBGAL_RS16795-MONOMER
    BRENDAi3.2.1.81 7557
    SABIO-RKiQ9RGX8

    Miscellaneous databases

    EvolutionaryTraceiQ9RGX8

    Family and domain databases

    CDDicd02178 GH16_beta_agarase, 1 hit
    InterProiView protein in InterPro
    IPR016287 Beta_agarase
    IPR013320 ConA-like_dom_sf
    IPR000757 GH16
    PfamiView protein in Pfam
    PF00722 Glyco_hydro_16, 1 hit
    PIRSFiPIRSF001097 Agarase, 1 hit
    SUPFAMiSSF49899 SSF49899, 1 hit
    PROSITEiView protein in PROSITE
    PS51762 GH16_2, 1 hit
    PS51257 PROKAR_LIPOPROTEIN, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiAGAB_ZOBGA
    AccessioniPrimary (citable) accession number: Q9RGX8
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 3, 2013
    Last sequence update: May 1, 2000
    Last modified: June 20, 2018
    This is version 89 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
      Index of protein domains and families
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
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