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Protein

Beta-agarase D

Gene

agaD

Organism
Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij)
Status
Reviewed-Annotation score: Annotation score: 3 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. Requires at least 4 consecutive agarose units and is highly intolerant to modifications.1 Publication

Catalytic activityi

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

Kineticsi

248 kcat is sec(-1).

  1. KM=6.5 mM for agarose1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei174NucleophileBy similarity1
    Binding sitei174SubstrateBy similarity1
    Active sitei179Proton donorBy similarity1
    Binding sitei179SubstrateBy similarity1
    Binding sitei206SubstrateBy similarity1
    Binding sitei340SubstrateBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Protein family/group databases

    CAZyiGH16. Glycoside Hydrolase Family 16.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Beta-agarase D (EC:3.2.1.81)
    Gene namesi
    Name:agaD
    Ordered Locus Names:zobellia_4243
    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

    Complete GO annotation...

    Keywords - Cellular componenti

    Secreted

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 20Sequence analysisAdd BLAST20
    ChainiPRO_000042202821 – 477Beta-agarase DAdd BLAST457

    Expressioni

    Inductioni

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

    Structurei

    Secondary structure

    1477
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni23 – 26Combined sources4
    Beta strandi38 – 41Combined sources4
    Turni43 – 45Combined sources3
    Beta strandi70 – 74Combined sources5
    Beta strandi91 – 93Combined sources3
    Beta strandi97 – 101Combined sources5
    Beta strandi104 – 110Combined sources7
    Beta strandi116 – 120Combined sources5
    Beta strandi124 – 130Combined sources7
    Beta strandi132 – 134Combined sources3
    Beta strandi136 – 141Combined sources6
    Beta strandi145 – 154Combined sources10
    Beta strandi157 – 167Combined sources11
    Beta strandi171 – 180Combined sources10
    Helixi191 – 194Combined sources4
    Beta strandi201 – 205Combined sources5
    Beta strandi211 – 213Combined sources3
    Helixi218 – 220Combined sources3
    Beta strandi234 – 243Combined sources10
    Beta strandi246 – 251Combined sources6
    Beta strandi254 – 260Combined sources7
    Beta strandi263 – 267Combined sources5
    Beta strandi273 – 278Combined sources6
    Beta strandi299 – 304Combined sources6
    Helixi305 – 311Combined sources7
    Beta strandi325 – 328Combined sources4
    Beta strandi333 – 340Combined sources8
    Helixi343 – 347Combined sources5
    Helixi354 – 357Combined sources4
    Helixi360 – 363Combined sources4
    Beta strandi364 – 376Combined sources13

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4ASMX-ray1.50B21-377[»]
    SMRiD7GXG4.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini22 – 378GH16PROSITE-ProRule annotationAdd BLAST357

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni94 – 104Substrate bindingBy similarityAdd BLAST11
    Regioni123 – 125Substrate bindingBy similarity3

    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

    OMAiWASRIPG.

    Family and domain databases

    Gene3Di2.60.120.200. 2 hits.
    InterProiIPR013320. ConA-like_dom.
    IPR000757. GH16.
    IPR026444. Secre_tail.
    [Graphical view]
    SUPFAMiSSF49899. SSF49899. 2 hits.
    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.

    D7GXG4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKRSILLAII AFLQFFTSYG QYDWDNVPIP ANAGAGKTWK LQTAASDDFN
    60 70 80 90 100
    YTFNPTNNVV DFGPNGNMKW YNKYHNRPNG QPNNFEGPGP TKWMQNHVAV
    110 120 130 140 150
    SGGNLNIWAS RIPGATKSFT GSNNTPISRP ETRAGCITNK TRVKYPVFVE
    160 170 180 190 200
    ARVKVMNSTL ASDIWLLSPD DTQEIDIMEC YGGPGNDNRN SYFASKIHLS
    210 220 230 240 250
    HHVFIRPPNF KDYQPADLNS WWGKNGVTQW GGKTIRIGVN WVSPTRLEYF
    260 270 280 290 300
    VDGQMVRILD NDAVQTRLAD GTWQYTYPAG VTSTGVNGQL IKENGYQKMN
    310 320 330 340 350
    IASSLSDAKN KSNISVIDPF NYLNNGRKFS KEMDIIINVE DQSWQAEAYR
    360 370 380 390 400
    SPNAAEMANF YDNNLLVDWI RVYKPVNASA ANSAETTSTV EKPASFEPQG
    410 420 430 440 450
    QPTEKLQVYP VPATDVLNIS QSDYVEARVY NLKGWVMLRK DVIDQKIDVS
    460 470
    SLKKGIYILE ITKATGETVK QKIVISE
    Length:477
    Mass (Da):53,522
    Last modified:August 10, 2010 - v1
    Checksum:iFC7C1359500450F5
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    FQ073842 Genomic DNA. Translation: CBM41186.1.
    FP476056 Genomic DNA. Translation: CAZ98378.1.
    RefSeqiWP_013995566.1. NC_015844.1.

    Genome annotation databases

    EnsemblBacteriaiCAZ98378; CAZ98378; ZOBELLIA_4243.
    KEGGizga:ZOBELLIA_4243.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    FQ073842 Genomic DNA. Translation: CBM41186.1.
    FP476056 Genomic DNA. Translation: CAZ98378.1.
    RefSeqiWP_013995566.1. NC_015844.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4ASMX-ray1.50B21-377[»]
    SMRiD7GXG4.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein family/group databases

    CAZyiGH16. Glycoside Hydrolase Family 16.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAZ98378; CAZ98378; ZOBELLIA_4243.
    KEGGizga:ZOBELLIA_4243.

    Phylogenomic databases

    OMAiWASRIPG.

    Family and domain databases

    Gene3Di2.60.120.200. 2 hits.
    InterProiIPR013320. ConA-like_dom.
    IPR000757. GH16.
    IPR026444. Secre_tail.
    [Graphical view]
    SUPFAMiSSF49899. SSF49899. 2 hits.
    TIGRFAMsiTIGR04183. Por_Secre_tail. 1 hit.
    PROSITEiPS51762. GH16_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiAGAD_ZOBGA
    AccessioniPrimary (citable) accession number: D7GXG4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 3, 2013
    Last sequence update: August 10, 2010
    Last modified: November 2, 2016
    This is version 35 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.