AGAB_ZOBGA
ID AGAB_ZOBGA Reviewed; 353 AA.
AC Q9RGX8;
DT 03-APR-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 102.
DE RecName: Full=Beta-agarase B;
DE EC=3.2.1.81;
DE Flags: Precursor;
GN Name=agaB; OrderedLocusNames=zobellia_3573;
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], FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND SUBCELLULAR LOCATION.
RC STRAIN=DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij;
RX PubMed=15456406; DOI=10.1042/bj20041044;
RA Jam M., Flament D., Allouch J., Potin P., Thion L., Kloareg B., Czjzek M.,
RA Helbert W., Michel G., Barbeyron T.;
RT "The endo-beta-agarases AgaA and AgaB from the marine bacterium Zobellia
RT galactanivorans: two paralogue enzymes with different molecular
RT organizations and catalytic behaviours.";
RL Biochem. J. 385:703-713(2005).
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 (2.30 ANGSTROMS) OF 19-353.
RX PubMed=12970344; DOI=10.1074/jbc.m308313200;
RA Allouch J., Jam M., Helbert W., Barbeyron T., Kloareg B., Henrissat B.,
RA Czjzek M.;
RT "The three-dimensional structures of two beta-agarases.";
RL J. Biol. Chem. 278:47171-47180(2003).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 53-353 OF MUTANT ASP-189 IN
RP COMPLEX WITH NEOAGAROOCTAOSE, FUNCTION, CATALYTIC ACTIVITY, AND INDUCTION.
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. Also tolerant to hybrid substrates
CC containing C6-sulfate groups at the -4, +1, and +3 positions.
CC {ECO:0000269|PubMed:15456406, 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:15456406, ECO:0000269|PubMed:22778272};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1 mM for agarose {ECO:0000269|PubMed:15456406};
CC Note=kcat is 100 sec(-1).;
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15456406,
CC ECO:0000269|PubMed:22778272}.
CC -!- SUBCELLULAR LOCATION: Cell outer membrane
CC {ECO:0000305|PubMed:15456406}; Lipid-anchor
CC {ECO:0000305|PubMed:15456406}.
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; AF098955; AAF21821.1; -; Genomic_DNA.
DR EMBL; FP476056; CAZ97711.1; -; Genomic_DNA.
DR RefSeq; WP_013994901.1; NC_015844.1.
DR PDB; 1O4Z; X-ray; 2.30 A; A/B/C/D=19-353.
DR PDB; 4ATF; X-ray; 1.90 A; A/B/C/D=53-353.
DR PDBsum; 1O4Z; -.
DR PDBsum; 4ATF; -.
DR AlphaFoldDB; Q9RGX8; -.
DR SMR; Q9RGX8; -.
DR STRING; 63186.ZOBELLIA_3573; -.
DR CAZy; GH16; Glycoside Hydrolase Family 16.
DR PRIDE; Q9RGX8; -.
DR EnsemblBacteria; CAZ97711; CAZ97711; ZOBELLIA_3573.
DR KEGG; zga:ZOBELLIA_3573; -.
DR PATRIC; fig|63186.3.peg.3487; -.
DR HOGENOM; CLU_037753_0_0_10; -.
DR OMA; CITSKEQ; -.
DR OrthoDB; 1046649at2; -.
DR BioCyc; MetaCyc:MON-16650; -.
DR BRENDA; 3.2.1.81; 7557.
DR SABIO-RK; Q9RGX8; -.
DR EvolutionaryTrace; Q9RGX8; -.
DR Proteomes; UP000008898; Chromosome.
DR GO; GO:0009279; C:cell outer membrane; TAS:UniProtKB.
DR GO; GO:0033916; F:beta-agarase activity; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0005975; P:carbohydrate metabolic process; IDA:UniProtKB.
DR CDD; cd02178; GH16_beta_agarase; 1.
DR InterPro; IPR016287; Beta_agarase.
DR InterPro; IPR013320; ConA-like_dom_sf.
DR InterPro; IPR000757; GH16.
DR Pfam; PF00722; Glyco_hydro_16; 1.
DR PIRSF; PIRSF001097; Agarase; 1.
DR SUPFAM; SSF49899; SSF49899; 1.
DR PROSITE; PS51762; GH16_2; 1.
DR PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell outer membrane; Glycosidase; Hydrolase; Lipoprotein;
KW Membrane; Palmitate; Reference proteome; Signal.
FT SIGNAL 1..17
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT CHAIN 18..353
FT /note="Beta-agarase B"
FT /id="PRO_5000055270"
FT DOMAIN 58..353
FT /note="GH16"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01098"
FT REGION 30..58
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 32..55
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 184
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:G0L322"
FT ACT_SITE 189
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:G0L322"
FT BINDING 105..107
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22778272"
FT BINDING 181
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22778272"
FT BINDING 215
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22778272"
FT BINDING 219
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22778272"
FT BINDING 224
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22778272"
FT BINDING 226
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22778272"
FT BINDING 308
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22778272"
FT LIPID 18
FT /note="N-palmitoyl cysteine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT LIPID 18
FT /note="S-diacylglycerol cysteine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT MUTAGEN 189
FT /note="E->D: Abolishes beta-agarase activity."
FT HELIX 60..62
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 73..77
FT /evidence="ECO:0007829|PDB:4ATF"
FT HELIX 95..100
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 101..104
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 106..108
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 115..117
FT /evidence="ECO:0007829|PDB:4ATF"
FT HELIX 119..121
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 122..125
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 128..132
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 142..144
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 146..151
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 155..164
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 167..178
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 181..191
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 194..196
FT /evidence="ECO:0007829|PDB:4ATF"
FT TURN 197..200
FT /evidence="ECO:0007829|PDB:4ATF"
FT HELIX 204..207
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 214..218
FT /evidence="ECO:0007829|PDB:4ATF"
FT TURN 219..222
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 223..225
FT /evidence="ECO:0007829|PDB:4ATF"
FT HELIX 230..232
FT /evidence="ECO:0007829|PDB:4ATF"
FT HELIX 240..242
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 245..253
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 256..261
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 264..271
FT /evidence="ECO:0007829|PDB:4ATF"
FT HELIX 272..275
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 282..285
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 301..308
FT /evidence="ECO:0007829|PDB:4ATF"
FT HELIX 311..314
FT /evidence="ECO:0007829|PDB:4ATF"
FT HELIX 321..323
FT /evidence="ECO:0007829|PDB:4ATF"
FT HELIX 329..332
FT /evidence="ECO:0007829|PDB:4ATF"
FT HELIX 336..338
FT /evidence="ECO:0007829|PDB:4ATF"
FT STRAND 339..352
FT /evidence="ECO:0007829|PDB:4ATF"
SQ SEQUENCE 353 AA; 40675 MW; 2281286B0F30F9FC CRC64;
MYLIYLRLVF CCALLLGCGD NSKFDSATDL PVEQEQEQET EQEGEPEESS EQDLVEEVDW
KDIPVPADAG PNMKWEFQEI SDNFEYEAPA DNKGSEFLEK WDDFYHNAWA GPGLTEWKRD
RSYVADGELK MWATRKPGSD KINMGCITSK TRVVYPVYIE ARAKVMNSTL ASDVWLLSAD
DTQEIDILEA YGADYSESAG KDHSYFSKKV HISHHVFIRD PFQDYQPKDA GSWFEDGTVW
NKEFHRFGVY WRDPWHLEYY IDGVLVRTVS GKDIIDPKHF TNTTDPGNTE IDTRTGLNKE
MDIIINTEDQ TWRSSPASGL QSNTYTPTDN ELSNIENNTF GVDWIRIYKP VEK
