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Protein

Xanthan lyase

Gene

xly

Organism
Bacillus sp. (strain GL1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Plays a role in xanthan depolymerization pathway by cleaving the linkage between the terminal mannosyl and glucuronyl residues of the side chain of xanthan to liberate pyruvylated mannose.3 Publications

Catalytic activityi

Eliminative cleavage of the terminal beta-D-mannosyl-(1->4)-beta-D-glucuronosyl linkage of the side-chain of the polysaccharide xanthan, leaving a 4-deoxy-alpha-L-threo-hex-4-enuronosyl group at the terminus of the side-chain.3 Publications

Enzyme regulationi

Highly specific for pyruvylated xanthan but not effective with hyaluronate, chondroitin A, gellan, heparin or pectin. Affinity for pyruvylated mannose is 400-fold stronger in comparison with mannose. Activated by Co2+ at 1 mM. Completely inhibited by Hg2+ but not affected by other divalent cations. Intensely inhibited by NaCl and KCl at 150 mM, in particular by the Na+ and K+ ions but not the Cl- ions. Partially inhibited by iodoacetamide and N-ethylmaleimide at 1 mM but not by dithiothreitol, reduced glutathione or 2-mercaptoethanol.3 Publications

Kineticsi

  1. KM=0.25 mM for xanthan2 Publications

    pH dependencei

    Optimum pH is 5.5 (in the presence of sodium acetate). Active between pH 6.5 and 9.2 Publications

    Temperature dependencei

    Optimum temperature is 50 degrees Celsius. Stable at 4 degrees Celsius at pH 6.5 - 9. 60% loss of activity when incubated at 45 degrees Celsius and pH 7.0 for 10 minutes.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei148 – 1481Carbohydrate1 Publication
    Binding sitei148 – 1481Substrate 12 Publications
    Binding sitei246 – 2461Substrate 21 Publication
    Binding sitei255 – 2551Carbohydrate1 Publication
    Binding sitei255 – 2551Substrate 12 Publications
    Binding sitei309 – 3091Carbohydrate1 Publication
    Binding sitei309 – 3091Substrate 1 and 22 Publications
    Binding sitei313 – 3131Carbohydrate1 Publication
    Binding sitei424 – 4241Substrate 21 Publication
    Metal bindingi515 – 5151Calcium2 Publications
    Metal bindingi516 – 5161Calcium2 Publications
    Metal bindingi517 – 5171Calcium2 Publications
    Binding sitei612 – 6121Substrate 1 and 22 Publications
    Metal bindingi676 – 6761Calcium2 Publications

    GO - Molecular functioni

    • calcium ion binding Source: UniProtKB
    • mannose binding Source: UniProtKB
    • xanthan lyase activity Source: UniProtKB

    GO - Biological processi

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

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Calcium, Metal-binding

    Protein family/group databases

    CAZyiPL8. Polysaccharide Lyase Family 8.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Xanthan lyaseImported (EC:4.2.2.121 Publication)
    Gene namesi
    Name:xlyImported
    OrganismiBacillus sp. (strain GL1)
    Taxonomic identifieri84635 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

    Subcellular locationi

    • Secretedextracellular space 1 Publication

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Secreted

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi194 – 1941N → A: Loss of activity by 60%. 1 Publication
    Mutagenesisi246 – 2461H → A: Loss of activity by 60%. 1 Publication
    Mutagenesisi255 – 2551Y → F: Loss of activity by 50%. 1 Publication
    Mutagenesisi313 – 3131R → A: Reduced catalytic activity. 1 Publication
    Mutagenesisi315 – 3151Y → F: Negligible change in catalytic activity. 1 Publication
    Mutagenesisi612 – 6121R → A: Increased catalysis rate but decreased affinity with substrate. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 25251 PublicationAdd
    BLAST
    Chaini26 – 930905Xanthan lyaseSequence AnalysisPRO_0000417933Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.4 Publications

    Structurei

    Secondary structure

    1
    930
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi28 – 4114Combined sources
    Turni43 – 453Combined sources
    Helixi51 – 7020Combined sources
    Helixi82 – 843Combined sources
    Helixi90 – 10819Combined sources
    Turni113 – 1164Combined sources
    Helixi118 – 13417Combined sources
    Beta strandi144 – 1463Combined sources
    Helixi147 – 1515Combined sources
    Helixi153 – 16412Combined sources
    Helixi166 – 1683Combined sources
    Helixi171 – 18414Combined sources
    Helixi192 – 20918Combined sources
    Helixi212 – 22110Combined sources
    Beta strandi227 – 2293Combined sources
    Beta strandi232 – 2376Combined sources
    Beta strandi243 – 2453Combined sources
    Turni246 – 2483Combined sources
    Turni252 – 2543Combined sources
    Helixi255 – 27016Combined sources
    Helixi280 – 2834Combined sources
    Helixi284 – 2918Combined sources
    Helixi294 – 2963Combined sources
    Helixi304 – 3063Combined sources
    Helixi308 – 3125Combined sources
    Helixi314 – 3163Combined sources
    Helixi318 – 33215Combined sources
    Turni333 – 3353Combined sources
    Helixi340 – 35415Combined sources
    Helixi360 – 3634Combined sources
    Helixi366 – 37611Combined sources
    Beta strandi389 – 3935Combined sources
    Helixi394 – 3963Combined sources
    Beta strandi398 – 4036Combined sources
    Beta strandi406 – 4116Combined sources
    Beta strandi415 – 4173Combined sources
    Turni431 – 4344Combined sources
    Beta strandi435 – 4417Combined sources
    Turni445 – 4484Combined sources
    Beta strandi449 – 4513Combined sources
    Helixi452 – 4554Combined sources
    Beta strandi465 – 4673Combined sources
    Beta strandi474 – 4763Combined sources
    Beta strandi482 – 4876Combined sources
    Turni488 – 4903Combined sources
    Beta strandi491 – 4999Combined sources
    Beta strandi501 – 5033Combined sources
    Beta strandi506 – 5138Combined sources
    Beta strandi518 – 5269Combined sources
    Beta strandi529 – 54113Combined sources
    Beta strandi550 – 5523Combined sources
    Beta strandi555 – 5573Combined sources
    Beta strandi563 – 57513Combined sources
    Beta strandi578 – 5825Combined sources
    Beta strandi585 – 60420Combined sources
    Helixi606 – 6083Combined sources
    Beta strandi620 – 63415Combined sources
    Beta strandi636 – 64611Combined sources
    Helixi650 – 6589Combined sources
    Beta strandi661 – 67616Combined sources
    Turni677 – 6804Combined sources
    Beta strandi681 – 6866Combined sources
    Beta strandi688 – 6903Combined sources
    Beta strandi692 – 6943Combined sources
    Beta strandi697 – 71014Combined sources
    Turni711 – 7133Combined sources
    Beta strandi714 – 7207Combined sources
    Beta strandi727 – 73610Combined sources
    Beta strandi738 – 7436Combined sources
    Beta strandi747 – 7515Combined sources
    Beta strandi753 – 7619Combined sources
    Beta strandi769 – 7768Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1J0MX-ray2.30A26-777[»]
    1J0NX-ray2.40A26-777[»]
    1X1HX-ray2.30A26-777[»]
    1X1IX-ray1.80A26-777[»]
    1X1JX-ray2.10A26-777[»]
    2E22X-ray2.40A26-777[»]
    2E24X-ray2.15A26-777[»]
    ProteinModelPortaliQ9AQS0.
    SMRiQ9AQS0. Positions 26-777.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9AQS0.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni146 – 1483Substrate binding1 Publication
    Regioni313 – 3153Substrate binding2 Publications

    Sequence similaritiesi

    Belongs to the polysaccharide lyase 8 family.Sequence Analysis

    Keywords - Domaini

    Signal

    Family and domain databases

    Gene3Di1.50.10.100. 1 hit.
    2.60.220.10. 1 hit.
    2.70.98.10. 1 hit.
    InterProiIPR008929. Chondroitin_lyas.
    IPR011013. Gal_mutarotase_SF_dom.
    IPR014718. Glyco_hydro-type_carb-bd_sub.
    IPR011071. Lyase_8-like_C.
    IPR012970. Lyase_8_alpha_N.
    IPR004103. Lyase_8_C.
    IPR003159. Lyase_8_central_dom.
    IPR012329. Lyase_8_N.
    [Graphical view]
    PfamiPF02278. Lyase_8. 1 hit.
    PF02884. Lyase_8_C. 1 hit.
    PF08124. Lyase_8_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF48230. SSF48230. 1 hit.
    SSF49863. SSF49863. 1 hit.
    SSF74650. SSF74650. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q9AQS0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLSGILIAAL LMTLWGGWQP DIAHASDEFD ALRIKWATLL TGGPALDPAD
    60 70 80 90 100
    SDIAARTDKL AQDANDYWED MDLSSSRTYI WYALRGNGTS DNVNAVYERL
    110 120 130 140 150
    RTMALAATTV GSSLYGNADL KEDILDALDW LYVNSYNSTR SRSAYNWWHW
    160 170 180 190 200
    QLGIPMSLND IAVLLYDDIS AARMATYMDT IDYFTPSIGL TGANRAWQAI
    210 220 230 240 250
    VVGVRAVIVK DAVKLAAARN GLSGTGIFPY ATGGDGFYAD GSFVQHTTFA
    260 270 280 290 300
    YTGGYGSSVL ETTANLMYLL SGSTWSVSDP NQSNVWQWIY EAYRPLLYKG
    310 320 330 340 350
    AMMDMVRGRE ISRSYAQDHA VGHGIVASIV RLAQFAPAPH AAAFKQIAKR
    360 370 380 390 400
    VIQEDTFSSF YGDVSTDTIR LAKAIVDDPS IAPAAAPNLY KQYAAMDRAV
    410 420 430 440 450
    LQRPGFALGL ALYSTRISSY ESINSENGRG WYTGAGATYL YNQDLAQYSE
    460 470 480 490 500
    DYWPTVDAYR IPGTTVASGT PIASGTGTSS WTGGVSLAGQ YGASGMDLSY
    510 520 530 540 550
    GAYNLSARKS WFMFDDEIVA LGSGISSTAG IPIETVVDNR KLNGAGDNAW
    560 570 580 590 600
    TANGAALSTG LGVAQTLTGV NWVHLAGNTA DGSDIGYYFP GGATLQTKRE
    610 620 630 640 650
    ARTGTWKQIN NRPATPSTAV TRNYETMWID HGTNPSGASY GYVLLPNKTS
    660 670 680 690 700
    AQVGAYAADP AIEIVVNTSG VQSVKEKTLG LVGANFWTDT TQTADLITSN
    710 720 730 740 750
    KKASVMTREI ADERLEASVS DPTQANNGTI AIELARSAEG YSADPGITVT
    760 770 780 790 800
    QLAPTIKFTV NVNGAKGKSF HASFQLGEDT SGPVDPGEPE LPSVIVDNAD
    810 820 830 840 850
    SAGVTRTGTW KTASTQTDRY GANYLHDDNA GKGTKSVTFT PNLPIAGSYE
    860 870 880 890 900
    VYLMWPAHFN REDAVQVDVG HASGTTRTAV DQRSGGGVWH SIGTYEFLAG
    910 920 930
    SGGSVTIRND ALGSPDGYVV ADAVKFVAVG
    Length:930
    Mass (Da):99,313
    Last modified:June 1, 2001 - v1
    Checksum:i5E8B69D3E94019C4
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB037178 Genomic DNA. Translation: BAB21059.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB037178 Genomic DNA. Translation: BAB21059.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1J0MX-ray2.30A26-777[»]
    1J0NX-ray2.40A26-777[»]
    1X1HX-ray2.30A26-777[»]
    1X1IX-ray1.80A26-777[»]
    1X1JX-ray2.10A26-777[»]
    2E22X-ray2.40A26-777[»]
    2E24X-ray2.15A26-777[»]
    ProteinModelPortaliQ9AQS0.
    SMRiQ9AQS0. Positions 26-777.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein family/group databases

    CAZyiPL8. Polysaccharide Lyase Family 8.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9AQS0.

    Family and domain databases

    Gene3Di1.50.10.100. 1 hit.
    2.60.220.10. 1 hit.
    2.70.98.10. 1 hit.
    InterProiIPR008929. Chondroitin_lyas.
    IPR011013. Gal_mutarotase_SF_dom.
    IPR014718. Glyco_hydro-type_carb-bd_sub.
    IPR011071. Lyase_8-like_C.
    IPR012970. Lyase_8_alpha_N.
    IPR004103. Lyase_8_C.
    IPR003159. Lyase_8_central_dom.
    IPR012329. Lyase_8_N.
    [Graphical view]
    PfamiPF02278. Lyase_8. 1 hit.
    PF02884. Lyase_8_C. 1 hit.
    PF08124. Lyase_8_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF48230. SSF48230. 1 hit.
    SSF49863. SSF49863. 1 hit.
    SSF74650. SSF74650. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Polysaccharide lyase: molecular cloning, sequencing, and overexpression of the xanthan lyase gene of Bacillus sp. strain GL1."
      Hashimoto W., Miki H., Tsuchiya N., Nankai H., Murata K.
      Appl. Environ. Microbiol. 67:713-720(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 26-35; 315-323; 332-341 AND 374-383, FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, SUBUNIT.
    2. "Xanthan lyase of Bacillus sp. strain GL1 liberates pyruvylated mannose from xanthan side chains."
      Hashimoto W., Miki H., Tsuchiya N., Nankai H., Murata K.
      Appl. Environ. Microbiol. 64:3765-3768(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, SUBCELLULAR LOCATION.
    3. "Microbial system for polysaccharide depolymerization: enzymatic route for xanthan depolymerization by Bacillus sp. strain GL1."
      Nankai H., Hashimoto W., Miki H., Kawai S., Murata K.
      Appl. Environ. Microbiol. 65:2520-2526(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    4. "Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan."
      Hashimoto W., Nankai H., Mikami B., Murata K.
      J. Biol. Chem. 278:7663-7673(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 26-777 IN COMPLEX WITH PYRUVYLATED MANNOSE AND CALCIUM.
    5. "Crystal structure of Bacillus sp. GL1 xanthan lyase complexed with a substrate: insights into the enzyme reaction mechanism."
      Maruyama Y., Hashimoto W., Mikami B., Murata K.
      J. Mol. Biol. 350:974-986(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF MUTANT ASN-194 IN COMPLEXES WITH PYRUVYLATED MANNOSE; PENTASACCHARIDE COMPLEX AND CALCIUM, MUTAGENESIS OF ASN-194; HIS-246 AND TYR-255, BIOPHYSICOCHEMICAL PROPERTIES.
    6. "A structural factor responsible for substrate recognition by Bacillus sp. GL1 xanthan lyase that acts specifically on pyruvated side chains of xanthan."
      Maruyama Y., Mikami B., Hashimoto W., Murata K.
      Biochemistry 46:781-791(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 26-777 IN COMPLEX WITH MANNOSE AND MUTANT ARG-612, MUTAGENESIS OF ARG-313; TYR-315 AND ARG-612, ENZYME REGULATION.

    Entry informationi

    Entry nameiXANLY_BACGL
    AccessioniPrimary (citable) accession number: Q9AQS0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 13, 2012
    Last sequence update: June 1, 2001
    Last modified: May 27, 2015
    This is version 63 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The 99 kDa precursor is converted to a mature form (77 kDa) through the removal of a C-terminal (22 kDa) fragment without any loss in activity.Curated

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.