AGAD_ZOBGA
ID AGAD_ZOBGA Reviewed; 477 AA.
AC D7GXG4;
DT 03-APR-2013, integrated into UniProtKB/Swiss-Prot.
DT 10-AUG-2010, sequence version 1.
DT 03-AUG-2022, entry version 56.
DE RecName: Full=Beta-agarase D;
DE EC=3.2.1.81;
DE Flags: Precursor;
GN Name=agaD; OrderedLocusNames=zobellia_4243;
OS Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 /
OS NCIMB 13871 / Dsij).
OC Bacteria; Bacteroidetes; Flavobacteriia; Flavobacteriales;
OC Flavobacteriaceae; Zobellia.
OX NCBI_TaxID=63186;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij;
RX PubMed=20376150; DOI=10.1038/nature08937;
RA Hehemann J.H., Correc G., Barbeyron T., Helbert W., Czjzek M., Michel G.;
RT "Transfer of carbohydrate-active enzymes from marine bacteria to Japanese
RT gut microbiota.";
RL Nature 464:908-912(2010).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij;
RG Genoscope - CEA;
RT "Complete genome sequence of Zobellia galactanivorans Dsij.";
RL Submitted (JUL-2009) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF 21-377, FUNCTION, CATALYTIC
RP ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, INDUCTION, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij;
RX PubMed=22778272; DOI=10.1074/jbc.m112.377184;
RA Hehemann J.H., Correc G., Thomas F., Bernard T., Barbeyron T., Jam M.,
RA Helbert W., Michel G., Czjzek M.;
RT "Biochemical and structural characterization of the complex agarolytic
RT enzyme system from the marine bacterium Zobellia galactanivorans.";
RL J. Biol. Chem. 287:30571-30584(2012).
CC -!- FUNCTION: Cleaves the beta-1,4-linkages between beta-D-galactose and
CC alpha-L-3,6-anhydro-galactose residues in agarose. Cleaves agarose in a
CC random manner with retention of the anomeric-bond configuration,
CC producing beta-anomers that give rise progressively to alpha-anomers
CC when mutarotation takes place. Requires at least 4 consecutive agarose
CC units and is highly intolerant to modifications.
CC {ECO:0000269|PubMed:22778272}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of (1->4)-beta-D-galactosidic linkages in agarose,
CC giving the tetramer as the predominant product.; EC=3.2.1.81;
CC Evidence={ECO:0000269|PubMed:22778272};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=6.5 mM for agarose {ECO:0000269|PubMed:22778272};
CC Note=248 kcat is sec(-1).;
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000305|PubMed:22778272}.
CC -!- INDUCTION: When cells are grown with the low sulfated agar.
CC {ECO:0000269|PubMed:22778272}.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 16 family. {ECO:0000305}.
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DR EMBL; FQ073842; CBM41186.1; -; Genomic_DNA.
DR EMBL; FP476056; CAZ98378.1; -; Genomic_DNA.
DR RefSeq; WP_013995566.1; NC_015844.1.
DR PDB; 4ASM; X-ray; 1.50 A; B=21-377.
DR PDBsum; 4ASM; -.
DR AlphaFoldDB; D7GXG4; -.
DR SMR; D7GXG4; -.
DR STRING; 63186.ZOBELLIA_4243; -.
DR CAZy; GH16; Glycoside Hydrolase Family 16.
DR EnsemblBacteria; CAZ98378; CAZ98378; ZOBELLIA_4243.
DR KEGG; zga:ZOBELLIA_4243; -.
DR PATRIC; fig|63186.3.peg.4154; -.
DR HOGENOM; CLU_037753_0_0_10; -.
DR OMA; WASRIPG; -.
DR OrthoDB; 1046649at2; -.
DR SABIO-RK; D7GXG4; -.
DR Proteomes; UP000008898; Chromosome.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0033916; F:beta-agarase activity; IEA:UniProtKB-EC.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:InterPro.
DR InterPro; IPR013320; ConA-like_dom_sf.
DR InterPro; IPR000757; GH16.
DR InterPro; IPR026444; Secre_tail.
DR Pfam; PF18962; Por_Secre_tail; 1.
DR SUPFAM; SSF49899; SSF49899; 2.
DR TIGRFAMs; TIGR04183; Por_Secre_tail; 1.
DR PROSITE; PS51762; GH16_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Glycosidase; Hydrolase; Reference proteome; Secreted; Signal.
FT SIGNAL 1..20
FT /evidence="ECO:0000255"
FT CHAIN 21..477
FT /note="Beta-agarase D"
FT /id="PRO_0000422028"
FT DOMAIN 22..378
FT /note="GH16"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01098"
FT REGION 382..402
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 174
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:G0L322"
FT ACT_SITE 179
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:G0L322"
FT BINDING 94..104
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:G0L322"
FT BINDING 123..125
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:G0L322"
FT BINDING 174
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:D7GXG0"
FT BINDING 179
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:D7GXG0"
FT BINDING 206
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:G0L322"
FT BINDING 340
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:D7GXG0"
FT TURN 23..26
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 38..41
FT /evidence="ECO:0007829|PDB:4ASM"
FT TURN 43..45
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 70..74
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 97..101
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 104..110
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 116..120
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 124..130
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 136..141
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 145..154
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 157..167
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 171..180
FT /evidence="ECO:0007829|PDB:4ASM"
FT HELIX 191..194
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 201..205
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 211..213
FT /evidence="ECO:0007829|PDB:4ASM"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 234..243
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 246..251
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 254..260
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 263..267
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 273..278
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 299..304
FT /evidence="ECO:0007829|PDB:4ASM"
FT HELIX 305..311
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 325..328
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 333..340
FT /evidence="ECO:0007829|PDB:4ASM"
FT HELIX 343..347
FT /evidence="ECO:0007829|PDB:4ASM"
FT HELIX 354..357
FT /evidence="ECO:0007829|PDB:4ASM"
FT HELIX 360..363
FT /evidence="ECO:0007829|PDB:4ASM"
FT STRAND 364..376
FT /evidence="ECO:0007829|PDB:4ASM"
SQ SEQUENCE 477 AA; 53522 MW; FC7C1359500450F5 CRC64;
MKRSILLAII AFLQFFTSYG QYDWDNVPIP ANAGAGKTWK LQTAASDDFN YTFNPTNNVV
DFGPNGNMKW YNKYHNRPNG QPNNFEGPGP TKWMQNHVAV SGGNLNIWAS RIPGATKSFT
GSNNTPISRP ETRAGCITNK TRVKYPVFVE ARVKVMNSTL ASDIWLLSPD DTQEIDIMEC
YGGPGNDNRN SYFASKIHLS HHVFIRPPNF KDYQPADLNS WWGKNGVTQW GGKTIRIGVN
WVSPTRLEYF VDGQMVRILD NDAVQTRLAD GTWQYTYPAG VTSTGVNGQL IKENGYQKMN
IASSLSDAKN KSNISVIDPF NYLNNGRKFS KEMDIIINVE DQSWQAEAYR SPNAAEMANF
YDNNLLVDWI RVYKPVNASA ANSAETTSTV EKPASFEPQG QPTEKLQVYP VPATDVLNIS
QSDYVEARVY NLKGWVMLRK DVIDQKIDVS SLKKGIYILE ITKATGETVK QKIVISE
