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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: 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)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

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

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16650.
    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 / 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
    Complete GO annotation...

    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

    • protein homodimerization activity Source: UniProtKB

    Structurei

    Secondary structure

    1353
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi60 – 62Combined sources3
    Beta strandi73 – 77Combined sources5
    Helixi95 – 100Combined sources6
    Beta strandi101 – 104Combined sources4
    Beta strandi106 – 108Combined sources3
    Beta strandi115 – 117Combined sources3
    Helixi119 – 121Combined sources3
    Beta strandi122 – 125Combined sources4
    Beta strandi128 – 132Combined sources5
    Beta strandi142 – 144Combined sources3
    Beta strandi146 – 151Combined sources6
    Beta strandi155 – 164Combined sources10
    Beta strandi167 – 178Combined sources12
    Beta strandi181 – 191Combined sources11
    Beta strandi194 – 196Combined sources3
    Turni197 – 200Combined sources4
    Helixi204 – 207Combined sources4
    Beta strandi214 – 218Combined sources5
    Turni219 – 222Combined sources4
    Beta strandi223 – 225Combined sources3
    Helixi230 – 232Combined sources3
    Helixi240 – 242Combined sources3
    Beta strandi245 – 253Combined sources9
    Beta strandi256 – 261Combined sources6
    Beta strandi264 – 271Combined sources8
    Helixi272 – 275Combined sources4
    Beta strandi282 – 285Combined sources4
    Beta strandi301 – 308Combined sources8
    Helixi311 – 314Combined sources4
    Helixi321 – 323Combined sources3
    Helixi329 – 332Combined sources4
    Helixi336 – 338Combined sources3
    Beta strandi339 – 352Combined sources14

    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...

    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
    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
    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.

    Phylogenomic databases

    KOiK01219.
    OMAiLASDVWL.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16650.
    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...

    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: November 2, 2016
    This is version 81 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.