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Beta-agarase B (EC 3.2.1.81)

 AGAB_ZOBGA              Reviewed;         353 AA.
Q9RGX8;
03-APR-2013, integrated into UniProtKB/Swiss-Prot.
01-MAY-2000, sequence version 1.
05-JUL-2017, entry version 85.
RecName: Full=Beta-agarase B;
EC=3.2.1.81;
Flags: Precursor;
Name=agaB; OrderedLocusNames=zobellia_3573;
Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 /
NCIMB 13871 / Dsij).
Bacteria; Bacteroidetes; Flavobacteriia; Flavobacteriales;
Flavobacteriaceae; Zobellia.
NCBI_TaxID=63186;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY,
BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND SUBCELLULAR LOCATION.
STRAIN=DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij;
PubMed=15456406; DOI=10.1042/BJ20041044;
Jam M., Flament D., Allouch J., Potin P., Thion L., Kloareg B.,
Czjzek M., Helbert W., Michel G., Barbeyron T.;
"The endo-beta-agarases AgaA and AgaB from the marine bacterium
Zobellia galactanivorans: two paralogue enzymes with different
molecular organizations and catalytic behaviours.";
Biochem. J. 385:703-713(2005).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij;
Genoscope - CEA;
"Complete genome sequence of Zobellia galactanivorans Dsij.";
Submitted (JUL-2009) to the EMBL/GenBank/DDBJ databases.
[3]
X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 19-353.
PubMed=12970344; DOI=10.1074/jbc.M308313200;
Allouch J., Jam M., Helbert W., Barbeyron T., Kloareg B.,
Henrissat B., Czjzek M.;
"The three-dimensional structures of two beta-agarases.";
J. Biol. Chem. 278:47171-47180(2003).
[4]
X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 53-353 OF MUTANT ASP-189 IN
COMPLEX WITH NEOAGAROOCTAOSE, FUNCTION, CATALYTIC ACTIVITY, AND
INDUCTION.
PubMed=22778272; DOI=10.1074/jbc.M112.377184;
Hehemann J.H., Correc G., Thomas F., Bernard T., Barbeyron T., Jam M.,
Helbert W., Michel G., Czjzek M.;
"Biochemical and structural characterization of the complex agarolytic
enzyme system from the marine bacterium Zobellia galactanivorans.";
J. Biol. Chem. 287:30571-30584(2012).
-!- FUNCTION: 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. {ECO:0000269|PubMed:15456406,
ECO:0000269|PubMed:22778272}.
-!- CATALYTIC ACTIVITY: Hydrolysis of (1->4)-beta-D-galactosidic
linkages in agarose, giving the tetramer as the predominant
product. {ECO:0000269|PubMed:15456406,
ECO:0000269|PubMed:22778272}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=1 mM for agarose {ECO:0000269|PubMed:15456406};
Note=kcat is 100 sec(-1).;
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15456406,
ECO:0000269|PubMed:22778272}.
-!- SUBCELLULAR LOCATION: Cell outer membrane
{ECO:0000305|PubMed:15456406}; Lipid-anchor
{ECO:0000305|PubMed:15456406}.
-!- INDUCTION: When cells are grown with the low sulfated agar.
{ECO:0000269|PubMed:22778272}.
-!- SIMILARITY: Belongs to the glycosyl hydrolase 16 family.
{ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; AF098955; AAF21821.1; -; Genomic_DNA.
EMBL; FP476056; CAZ97711.1; -; Genomic_DNA.
RefSeq; WP_013994901.1; NC_015844.1.
PDB; 1O4Z; X-ray; 2.30 A; A/B/C/D=19-353.
PDB; 4ATF; X-ray; 1.90 A; A/B/C/D=53-353.
PDBsum; 1O4Z; -.
PDBsum; 4ATF; -.
ProteinModelPortal; Q9RGX8; -.
SMR; Q9RGX8; -.
CAZy; GH16; Glycoside Hydrolase Family 16.
EnsemblBacteria; CAZ97711; CAZ97711; ZOBELLIA_3573.
KEGG; zga:ZOBELLIA_3573; -.
PATRIC; fig|63186.3.peg.3487; -.
KO; K01219; -.
OMA; LASDVWL; -.
BioCyc; MetaCyc:MONOMER-16650; -.
BRENDA; 3.2.1.81; 7557.
SABIO-RK; Q9RGX8; -.
EvolutionaryTrace; Q9RGX8; -.
Proteomes; UP000008898; Chromosome.
GO; GO:0009279; C:cell outer membrane; TAS:UniProtKB.
GO; GO:0033916; F:beta-agarase activity; IDA:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
GO; GO:0005975; P:carbohydrate metabolic process; IDA:UniProtKB.
GO; GO:0008152; P:metabolic process; IDA:UniProtKB.
CDD; cd02178; GH16_beta_agarase; 1.
InterPro; IPR016287; Beta_agarase.
InterPro; IPR013320; ConA-like_dom.
InterPro; IPR000757; GH16.
Pfam; PF00722; Glyco_hydro_16; 1.
PIRSF; PIRSF001097; Agarase; 1.
SUPFAM; SSF49899; SSF49899; 1.
PROSITE; PS51762; GH16_2; 1.
PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.
1: Evidence at protein level;
3D-structure; Cell outer membrane; Complete proteome; Glycosidase;
Hydrolase; Lipoprotein; Membrane; Palmitate; Reference proteome;
Signal.
SIGNAL 1 17 {ECO:0000255|PROSITE-ProRule:PRU00303}.
CHAIN 18 353 Beta-agarase B.
/FTId=PRO_5000055270.
DOMAIN 58 353 GH16. {ECO:0000255|PROSITE-
ProRule:PRU01098}.
REGION 105 107 Substrate binding.
{ECO:0000269|PubMed:22778272}.
ACT_SITE 184 184 Nucleophile.
{ECO:0000250|UniProtKB:G0L322}.
ACT_SITE 189 189 Proton donor.
{ECO:0000250|UniProtKB:G0L322}.
BINDING 181 181 Substrate. {ECO:0000269|PubMed:22778272}.
BINDING 215 215 Substrate. {ECO:0000269|PubMed:22778272}.
BINDING 219 219 Substrate. {ECO:0000269|PubMed:22778272}.
BINDING 224 224 Substrate. {ECO:0000269|PubMed:22778272}.
BINDING 226 226 Substrate. {ECO:0000269|PubMed:22778272}.
BINDING 308 308 Substrate. {ECO:0000269|PubMed:22778272}.
LIPID 18 18 N-palmitoyl cysteine.
{ECO:0000255|PROSITE-ProRule:PRU00303}.
LIPID 18 18 S-diacylglycerol cysteine.
{ECO:0000255|PROSITE-ProRule:PRU00303}.
MUTAGEN 189 189 E->D: Abolishes beta-agarase activity.
HELIX 60 62 {ECO:0000244|PDB:4ATF}.
STRAND 73 77 {ECO:0000244|PDB:4ATF}.
HELIX 95 100 {ECO:0000244|PDB:4ATF}.
STRAND 101 104 {ECO:0000244|PDB:4ATF}.
STRAND 106 108 {ECO:0000244|PDB:4ATF}.
STRAND 115 117 {ECO:0000244|PDB:4ATF}.
HELIX 119 121 {ECO:0000244|PDB:4ATF}.
STRAND 122 125 {ECO:0000244|PDB:4ATF}.
STRAND 128 132 {ECO:0000244|PDB:4ATF}.
STRAND 142 144 {ECO:0000244|PDB:4ATF}.
STRAND 146 151 {ECO:0000244|PDB:4ATF}.
STRAND 155 164 {ECO:0000244|PDB:4ATF}.
STRAND 167 178 {ECO:0000244|PDB:4ATF}.
STRAND 181 191 {ECO:0000244|PDB:4ATF}.
STRAND 194 196 {ECO:0000244|PDB:4ATF}.
TURN 197 200 {ECO:0000244|PDB:4ATF}.
HELIX 204 207 {ECO:0000244|PDB:4ATF}.
STRAND 214 218 {ECO:0000244|PDB:4ATF}.
TURN 219 222 {ECO:0000244|PDB:4ATF}.
STRAND 223 225 {ECO:0000244|PDB:4ATF}.
HELIX 230 232 {ECO:0000244|PDB:4ATF}.
HELIX 240 242 {ECO:0000244|PDB:4ATF}.
STRAND 245 253 {ECO:0000244|PDB:4ATF}.
STRAND 256 261 {ECO:0000244|PDB:4ATF}.
STRAND 264 271 {ECO:0000244|PDB:4ATF}.
HELIX 272 275 {ECO:0000244|PDB:4ATF}.
STRAND 282 285 {ECO:0000244|PDB:4ATF}.
STRAND 301 308 {ECO:0000244|PDB:4ATF}.
HELIX 311 314 {ECO:0000244|PDB:4ATF}.
HELIX 321 323 {ECO:0000244|PDB:4ATF}.
HELIX 329 332 {ECO:0000244|PDB:4ATF}.
HELIX 336 338 {ECO:0000244|PDB:4ATF}.
STRAND 339 352 {ECO:0000244|PDB:4ATF}.
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


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