XANLY_BACGL
ID XANLY_BACGL Reviewed; 930 AA.
AC Q9AQS0;
DT 13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=Xanthan lyase {ECO:0000312|EMBL:BAB21059.1};
DE EC=4.2.2.12 {ECO:0000269|PubMed:9758797};
DE Flags: Precursor;
GN Name=xly {ECO:0000312|EMBL:BAB21059.1};
OS Bacillus sp. (strain GL1).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=84635;
RN [1] {ECO:0000305, ECO:0000312|EMBL:BAB21059.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 26-35; 315-323;
RP 332-341 AND 374-383, FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND
RP SUBUNIT.
RX PubMed=11157235; DOI=10.1128/aem.67.2.713-720.2001;
RA Hashimoto W., Miki H., Tsuchiya N., Nankai H., Murata K.;
RT "Polysaccharide lyase: molecular cloning, sequencing, and overexpression of
RT the xanthan lyase gene of Bacillus sp. strain GL1.";
RL Appl. Environ. Microbiol. 67:713-720(2001).
RN [2] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL
RP PROPERTIES, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=9758797; DOI=10.1128/aem.64.10.3765-3768.1998;
RA Hashimoto W., Miki H., Tsuchiya N., Nankai H., Murata K.;
RT "Xanthan lyase of Bacillus sp. strain GL1 liberates pyruvylated mannose
RT from xanthan side chains.";
RL Appl. Environ. Microbiol. 64:3765-3768(1998).
RN [3] {ECO:0000305}
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=10347037; DOI=10.1128/aem.65.6.2520-2526.1999;
RA Nankai H., Hashimoto W., Miki H., Kawai S., Murata K.;
RT "Microbial system for polysaccharide depolymerization: enzymatic route for
RT xanthan depolymerization by Bacillus sp. strain GL1.";
RL Appl. Environ. Microbiol. 65:2520-2526(1999).
RN [4] {ECO:0000305, ECO:0000312|PDB:1J0N}
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 26-777 IN COMPLEX WITH
RP PYRUVYLATED MANNOSE AND CALCIUM.
RX PubMed=12475987; DOI=10.1074/jbc.m208100200;
RA Hashimoto W., Nankai H., Mikami B., Murata K.;
RT "Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the
RT side chains of xanthan.";
RL J. Biol. Chem. 278:7663-7673(2003).
RN [5] {ECO:0007744|PDB:1X1H, ECO:0007744|PDB:1X1I, ECO:0007744|PDB:1X1J}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF MUTANT ALA-194 IN COMPLEXES WITH
RP PYRUVYLATED MANNOSE; PENTASACCHARIDE AND CALCIUM, MUTAGENESIS OF ASN-194;
RP HIS-246 AND TYR-255, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, ACTIVE SITE, AND REACTION MECHANISM.
RX PubMed=15979090; DOI=10.1016/j.jmb.2005.05.055;
RA Maruyama Y., Hashimoto W., Mikami B., Murata K.;
RT "Crystal structure of Bacillus sp. GL1 xanthan lyase complexed with a
RT substrate: insights into the enzyme reaction mechanism.";
RL J. Mol. Biol. 350:974-986(2005).
RN [6] {ECO:0000305, ECO:0000312|PDB:2E22}
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 26-777 IN COMPLEX WITH MANNOSE
RP AND MUTANT ARG-612, MUTAGENESIS OF ARG-313; TYR-315 AND ARG-612, AND
RP ACTIVITY REGULATION.
RX PubMed=17223699; DOI=10.1021/bi0619775;
RA Maruyama Y., Mikami B., Hashimoto W., Murata K.;
RT "A structural factor responsible for substrate recognition by Bacillus sp.
RT GL1 xanthan lyase that acts specifically on pyruvated side chains of
RT xanthan.";
RL Biochemistry 46:781-791(2007).
CC -!- FUNCTION: Plays a role in xanthan depolymerization pathway by cleaving
CC the linkage between the terminal mannosyl and glucuronyl residues of
CC the side chain of xanthan to liberate pyruvylated mannose. Is highly
CC specific for pyruvylated side-chains of xanthan and is not effective
CC with hyaluronate, chondroitin A, gellan, heparin or pectin.
CC {ECO:0000269|PubMed:10347037, ECO:0000269|PubMed:11157235,
CC ECO:0000269|PubMed:15979090, ECO:0000269|PubMed:9758797}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Eliminative cleavage of the terminal beta-D-mannosyl-(1->4)-
CC beta-D-glucuronosyl linkage of the side-chain of the polysaccharide
CC xanthan, leaving a 4-deoxy-alpha-L-threo-hex-4-enuronosyl group at
CC the terminus of the side-chain.; EC=4.2.2.12;
CC Evidence={ECO:0000269|PubMed:10347037, ECO:0000269|PubMed:11157235,
CC ECO:0000269|PubMed:15979090, ECO:0000269|PubMed:9758797};
CC -!- ACTIVITY REGULATION: Activated by Co(2+) at 1 mM. Completely inhibited
CC by Hg(2+) but not affected by other divalent cations. Intensely
CC inhibited by NaCl and KCl at 150 mM, in particular by the Na(+) and
CC K(+) ions but not the Cl(-) ions. Partially inhibited by iodoacetamide
CC and N-ethylmaleimide at 1 mM but not by dithiothreitol, reduced
CC glutathione or 2-mercaptoethanol. {ECO:0000269|PubMed:11157235,
CC ECO:0000269|PubMed:17223699, ECO:0000269|PubMed:9758797}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.25 mM for xanthan {ECO:0000269|PubMed:15979090,
CC ECO:0000269|PubMed:9758797};
CC Note=kcat is 2170 sec(-1). {ECO:0000269|PubMed:15979090};
CC pH dependence:
CC Optimum pH is 5.5 (in the presence of sodium acetate). Active between
CC pH 6.5 and 9. {ECO:0000269|PubMed:15979090,
CC ECO:0000269|PubMed:9758797};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius. Stable at 4 degrees
CC Celsius at pH 6.5 - 9. 60% loss of activity when incubated at 45
CC degrees Celsius and pH 7.0 for 10 minutes.
CC {ECO:0000269|PubMed:15979090, ECO:0000269|PubMed:9758797};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:11157235,
CC ECO:0000269|PubMed:12475987, ECO:0000269|PubMed:17223699,
CC ECO:0000269|PubMed:9758797}.
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000269|PubMed:9758797}.
CC -!- MISCELLANEOUS: The 99 kDa precursor is converted to a mature form (77
CC kDa) through the removal of a C-terminal (22 kDa) fragment without any
CC loss in activity. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the polysaccharide lyase 8 family.
CC {ECO:0000255}.
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DR EMBL; AB037178; BAB21059.1; -; Genomic_DNA.
DR PDB; 1J0M; X-ray; 2.30 A; A=26-777.
DR PDB; 1J0N; X-ray; 2.40 A; A=26-777.
DR PDB; 1X1H; X-ray; 2.30 A; A=26-777.
DR PDB; 1X1I; X-ray; 1.80 A; A=26-777.
DR PDB; 1X1J; X-ray; 2.10 A; A=26-777.
DR PDB; 2E22; X-ray; 2.40 A; A=26-777.
DR PDB; 2E24; X-ray; 2.15 A; A=26-777.
DR PDBsum; 1J0M; -.
DR PDBsum; 1J0N; -.
DR PDBsum; 1X1H; -.
DR PDBsum; 1X1I; -.
DR PDBsum; 1X1J; -.
DR PDBsum; 2E22; -.
DR PDBsum; 2E24; -.
DR AlphaFoldDB; Q9AQS0; -.
DR SMR; Q9AQS0; -.
DR DrugBank; DB04386; 4,6-O-(1-Carboxyethylidene)-Beta-D-Glucose.
DR DrugBank; DB04597; 4,6-O-(1-CARBOXYETHYLIDENE)-BETA-D-MANNOSE.
DR DrugBank; DB04596; 4-O-{4,6-O-[(1S)-1-Carboxyethylidene]-Beta-D-mannopyranosyl}-D-glucopyranuronic acid.
DR CAZy; PL8; Polysaccharide Lyase Family 8.
DR EvolutionaryTrace; Q9AQS0; -.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0005509; F:calcium ion binding; IDA:UniProtKB.
DR GO; GO:0005537; F:mannose binding; IDA:UniProtKB.
DR GO; GO:0047492; F:xanthan lyase activity; IDA:UniProtKB.
DR GO; GO:0005976; P:polysaccharide metabolic process; IDA:UniProtKB.
DR CDD; cd14488; CBM6-CBM35-CBM36_like_2; 1.
DR Gene3D; 1.50.10.100; -; 1.
DR Gene3D; 2.60.220.10; -; 1.
DR Gene3D; 2.70.98.10; -; 1.
DR InterPro; IPR033803; CBM6/CBM35/CBM36-like_2.
DR InterPro; IPR008929; Chondroitin_lyas.
DR InterPro; IPR011013; Gal_mutarotase_sf_dom.
DR InterPro; IPR014718; GH-type_carb-bd.
DR InterPro; IPR038970; Lyase_8.
DR InterPro; IPR011071; Lyase_8-like_C.
DR InterPro; IPR012970; Lyase_8_alpha_N.
DR InterPro; IPR004103; Lyase_8_C.
DR InterPro; IPR003159; Lyase_8_central_dom.
DR PANTHER; PTHR38481; PTHR38481; 1.
DR Pfam; PF02278; Lyase_8; 1.
DR Pfam; PF02884; Lyase_8_C; 1.
DR Pfam; PF08124; Lyase_8_N; 1.
DR SUPFAM; SSF48230; SSF48230; 1.
DR SUPFAM; SSF49863; SSF49863; 1.
DR SUPFAM; SSF74650; SSF74650; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Direct protein sequencing; Lyase; Metal-binding;
KW Secreted; Signal.
FT SIGNAL 1..25
FT /evidence="ECO:0000269|PubMed:11157235"
FT CHAIN 26..930
FT /note="Xanthan lyase"
FT /evidence="ECO:0000255"
FT /id="PRO_0000417933"
FT ACT_SITE 255
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:15979090"
FT BINDING 146..148
FT /ligand="xanthan"
FT /ligand_id="ChEBI:CHEBI:189560"
FT /evidence="ECO:0000269|PubMed:15979090,
FT ECO:0007744|PDB:1X1J"
FT BINDING 246
FT /ligand="xanthan"
FT /ligand_id="ChEBI:CHEBI:189560"
FT /evidence="ECO:0000269|PubMed:15979090,
FT ECO:0007744|PDB:1X1J"
FT BINDING 255
FT /ligand="xanthan"
FT /ligand_id="ChEBI:CHEBI:189560"
FT /evidence="ECO:0000269|PubMed:15979090,
FT ECO:0007744|PDB:1X1J"
FT BINDING 309
FT /ligand="xanthan"
FT /ligand_id="ChEBI:CHEBI:189560"
FT /evidence="ECO:0000269|PubMed:15979090,
FT ECO:0007744|PDB:1X1J"
FT BINDING 313..315
FT /ligand="xanthan"
FT /ligand_id="ChEBI:CHEBI:189560"
FT /evidence="ECO:0000269|PubMed:15979090,
FT ECO:0007744|PDB:1X1J"
FT BINDING 424
FT /ligand="xanthan"
FT /ligand_id="ChEBI:CHEBI:189560"
FT /evidence="ECO:0000269|PubMed:15979090,
FT ECO:0007744|PDB:1X1J"
FT BINDING 515
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000269|PubMed:12475987,
FT ECO:0000269|PubMed:15979090"
FT BINDING 516
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000269|PubMed:12475987,
FT ECO:0000269|PubMed:15979090"
FT BINDING 517
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000269|PubMed:12475987,
FT ECO:0000269|PubMed:15979090"
FT BINDING 612
FT /ligand="xanthan"
FT /ligand_id="ChEBI:CHEBI:189560"
FT /evidence="ECO:0000269|PubMed:15979090,
FT ECO:0007744|PDB:1X1J"
FT BINDING 676
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000269|PubMed:12475987,
FT ECO:0000269|PubMed:15979090"
FT MUTAGEN 194
FT /note="N->A: Loss of activity by 60%."
FT /evidence="ECO:0000269|PubMed:15979090"
FT MUTAGEN 246
FT /note="H->A: Loss of activity by 60%."
FT /evidence="ECO:0000269|PubMed:15979090"
FT MUTAGEN 255
FT /note="Y->F: Loss of activity by 50%."
FT /evidence="ECO:0000269|PubMed:15979090"
FT MUTAGEN 313
FT /note="R->A: Reduced catalytic activity."
FT /evidence="ECO:0000269|PubMed:17223699"
FT MUTAGEN 315
FT /note="Y->F: Negligible change in catalytic activity."
FT /evidence="ECO:0000269|PubMed:17223699"
FT MUTAGEN 612
FT /note="R->A: Increased catalysis rate but decreased
FT affinity with substrate."
FT /evidence="ECO:0000269|PubMed:17223699"
FT HELIX 28..41
FT /evidence="ECO:0007829|PDB:1X1I"
FT TURN 43..45
FT /evidence="ECO:0007829|PDB:1J0M"
FT HELIX 51..70
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 90..108
FT /evidence="ECO:0007829|PDB:1X1I"
FT TURN 113..116
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 118..134
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 147..151
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 153..164
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 166..168
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 171..184
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 192..209
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 212..221
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 227..229
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 232..237
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 243..245
FT /evidence="ECO:0007829|PDB:1X1I"
FT TURN 246..248
FT /evidence="ECO:0007829|PDB:1X1I"
FT TURN 252..254
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 255..270
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 280..283
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 284..291
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 294..296
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 304..306
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 308..312
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 314..316
FT /evidence="ECO:0007829|PDB:1X1J"
FT HELIX 318..332
FT /evidence="ECO:0007829|PDB:1X1I"
FT TURN 333..335
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 340..354
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 360..363
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 366..376
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 389..393
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 394..396
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 398..403
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 406..411
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 415..417
FT /evidence="ECO:0007829|PDB:1X1I"
FT TURN 431..434
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 435..441
FT /evidence="ECO:0007829|PDB:1X1I"
FT TURN 445..448
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 449..451
FT /evidence="ECO:0007829|PDB:1X1J"
FT HELIX 452..455
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 465..467
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 474..476
FT /evidence="ECO:0007829|PDB:1J0M"
FT STRAND 482..487
FT /evidence="ECO:0007829|PDB:1X1I"
FT TURN 488..490
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 491..499
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 501..503
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 506..513
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 518..526
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 529..541
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 550..552
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 555..557
FT /evidence="ECO:0007829|PDB:2E24"
FT STRAND 563..575
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 578..582
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 585..604
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 606..608
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 620..634
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 636..646
FT /evidence="ECO:0007829|PDB:1X1I"
FT HELIX 650..658
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 661..676
FT /evidence="ECO:0007829|PDB:1X1I"
FT TURN 677..680
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 681..686
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 688..690
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 692..694
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 697..710
FT /evidence="ECO:0007829|PDB:1X1I"
FT TURN 711..713
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 714..720
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 727..736
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 738..743
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 747..751
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 753..761
FT /evidence="ECO:0007829|PDB:1X1I"
FT STRAND 769..776
FT /evidence="ECO:0007829|PDB:1X1I"
SQ SEQUENCE 930 AA; 99313 MW; 5E8B69D3E94019C4 CRC64;
MLSGILIAAL LMTLWGGWQP DIAHASDEFD ALRIKWATLL TGGPALDPAD SDIAARTDKL
AQDANDYWED MDLSSSRTYI WYALRGNGTS DNVNAVYERL RTMALAATTV GSSLYGNADL
KEDILDALDW LYVNSYNSTR SRSAYNWWHW QLGIPMSLND IAVLLYDDIS AARMATYMDT
IDYFTPSIGL TGANRAWQAI VVGVRAVIVK DAVKLAAARN GLSGTGIFPY ATGGDGFYAD
GSFVQHTTFA YTGGYGSSVL ETTANLMYLL SGSTWSVSDP NQSNVWQWIY EAYRPLLYKG
AMMDMVRGRE ISRSYAQDHA VGHGIVASIV RLAQFAPAPH AAAFKQIAKR VIQEDTFSSF
YGDVSTDTIR LAKAIVDDPS IAPAAAPNLY KQYAAMDRAV LQRPGFALGL ALYSTRISSY
ESINSENGRG WYTGAGATYL YNQDLAQYSE DYWPTVDAYR IPGTTVASGT PIASGTGTSS
WTGGVSLAGQ YGASGMDLSY GAYNLSARKS WFMFDDEIVA LGSGISSTAG IPIETVVDNR
KLNGAGDNAW TANGAALSTG LGVAQTLTGV NWVHLAGNTA DGSDIGYYFP GGATLQTKRE
ARTGTWKQIN NRPATPSTAV TRNYETMWID HGTNPSGASY GYVLLPNKTS AQVGAYAADP
AIEIVVNTSG VQSVKEKTLG LVGANFWTDT TQTADLITSN KKASVMTREI ADERLEASVS
DPTQANNGTI AIELARSAEG YSADPGITVT QLAPTIKFTV NVNGAKGKSF HASFQLGEDT
SGPVDPGEPE LPSVIVDNAD SAGVTRTGTW KTASTQTDRY GANYLHDDNA GKGTKSVTFT
PNLPIAGSYE VYLMWPAHFN REDAVQVDVG HASGTTRTAV DQRSGGGVWH SIGTYEFLAG
SGGSVTIRND ALGSPDGYVV ADAVKFVAVG
