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Q9AQS0

- XANLY_BACGL

UniProt

Q9AQS0 - XANLY_BACGL

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Protein

Xanthan lyase

Gene
xly
Organism
Bacillus sp. (strain GL1)
Status
Reviewed - 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 9.1 Publication

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.1 Publication

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

  1. calcium ion binding Source: UniProtKB
  2. mannose binding Source: UniProtKB
  3. xanthan lyase activity Source: UniProtKB

GO - Biological processi

  1. carbohydrate metabolic process Source: InterPro
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 lyase (EC:4.2.2.12)
Gene namesi
Name:xly
OrganismiBacillus sp. (strain GL1)
Taxonomic identifieri84635 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Subcellular locationi

Secretedextracellular space 1 Publication

GO - Cellular componenti

  1. extracellular space Source: UniProtKB-SubCell
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 lyasePRO_0000417933Add
BLAST

Interactioni

Subunit structurei

Monomer.2 Publications

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiQ9AQS0.

Family & Domainsi

Region

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

Sequence similaritiesi

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

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MLSGILIAAL LMTLWGGWQP DIAHASDEFD ALRIKWATLL TGGPALDPAD    50
SDIAARTDKL AQDANDYWED MDLSSSRTYI WYALRGNGTS DNVNAVYERL 100
RTMALAATTV GSSLYGNADL KEDILDALDW LYVNSYNSTR SRSAYNWWHW 150
QLGIPMSLND IAVLLYDDIS AARMATYMDT IDYFTPSIGL TGANRAWQAI 200
VVGVRAVIVK DAVKLAAARN GLSGTGIFPY ATGGDGFYAD GSFVQHTTFA 250
YTGGYGSSVL ETTANLMYLL SGSTWSVSDP NQSNVWQWIY EAYRPLLYKG 300
AMMDMVRGRE ISRSYAQDHA VGHGIVASIV RLAQFAPAPH AAAFKQIAKR 350
VIQEDTFSSF YGDVSTDTIR LAKAIVDDPS IAPAAAPNLY KQYAAMDRAV 400
LQRPGFALGL ALYSTRISSY ESINSENGRG WYTGAGATYL YNQDLAQYSE 450
DYWPTVDAYR IPGTTVASGT PIASGTGTSS WTGGVSLAGQ YGASGMDLSY 500
GAYNLSARKS WFMFDDEIVA LGSGISSTAG IPIETVVDNR KLNGAGDNAW 550
TANGAALSTG LGVAQTLTGV NWVHLAGNTA DGSDIGYYFP GGATLQTKRE 600
ARTGTWKQIN NRPATPSTAV TRNYETMWID HGTNPSGASY GYVLLPNKTS 650
AQVGAYAADP AIEIVVNTSG VQSVKEKTLG LVGANFWTDT TQTADLITSN 700
KKASVMTREI ADERLEASVS DPTQANNGTI AIELARSAEG YSADPGITVT 750
QLAPTIKFTV NVNGAKGKSF HASFQLGEDT SGPVDPGEPE LPSVIVDNAD 800
SAGVTRTGTW KTASTQTDRY GANYLHDDNA GKGTKSVTFT PNLPIAGSYE 850
VYLMWPAHFN REDAVQVDVG HASGTTRTAV DQRSGGGVWH SIGTYEFLAG 900
SGGSVTIRND ALGSPDGYVV ADAVKFVAVG 930
Length:930
Mass (Da):99,313
Last modified:June 1, 2001 - v1
Checksum:i5E8B69D3E94019C4
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB037178 Genomic DNA. Translation: BAB21059.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB037178 Genomic DNA. Translation: BAB21059.1 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1J0M X-ray 2.30 A 26-777 [» ]
1J0N X-ray 2.40 A 26-777 [» ]
1X1H X-ray 2.30 A 26-777 [» ]
1X1I X-ray 1.80 A 26-777 [» ]
1X1J X-ray 2.10 A 26-777 [» ]
2E22 X-ray 2.40 A 26-777 [» ]
2E24 X-ray 2.15 A 26-777 [» ]
ProteinModelPortali Q9AQS0.
SMRi Q9AQS0. Positions 26-777.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

CAZyi PL8. Polysaccharide Lyase Family 8.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei Q9AQS0.

Family and domain databases

Gene3Di 1.50.10.100. 1 hit.
2.60.220.10. 1 hit.
2.70.98.10. 1 hit.
InterProi IPR008929. 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 ]
Pfami PF02278. Lyase_8. 1 hit.
PF02884. Lyase_8_C. 1 hit.
PF08124. Lyase_8_N. 1 hit.
[Graphical view ]
SUPFAMi SSF48230. SSF48230. 1 hit.
SSF49863. SSF49863. 1 hit.
SSF74650. SSF74650. 1 hit.
ProtoNeti Search...

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: October 16, 2013
This is version 56 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.

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

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