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Q9AQS0 (XANLY_BACGL) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 55. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Xanthan lyase
EC=4.2.2.12
Gene names
Name:xly
OrganismBacillus sp. (strain GL1)
Taxonomic identifier84635 [NCBI]
Taxonomic lineageBacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length930 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.2 Ref.3

Catalytic activity

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. Ref.1 Ref.2 Ref.3

Enzyme regulation

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. Ref.1 Ref.2 Ref.6

Subunit structure

Monomer. Ref.1 Ref.2

Subcellular location

Secreted › extracellular space Ref.2.

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.

Sequence similarities

Belongs to the polysaccharide lyase 8 family.

Biophysicochemical properties

Kinetic parameters:

KM=0.25 mM for xanthan Ref.2 Ref.5

pH dependence:

Optimum pH is 5.5 (in the presence of sodium acetate). Active between pH 6.5 and 9. Ref.2

Temperature dependence:

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. Ref.2

Ontologies

Keywords
   Cellular componentSecreted
   DomainSignal
   LigandCalcium
Metal-binding
   Molecular functionLyase
   Technical term3D-structure
Direct protein sequencing
Gene Ontology (GO)
   Biological_processcarbohydrate metabolic process

Inferred from electronic annotation. Source: InterPro

   Cellular_componentextracellular space

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functioncalcium ion binding

Inferred from direct assay Ref.5. Source: UniProtKB

mannose binding

Inferred from direct assay Ref.6. Source: UniProtKB

xanthan lyase activity

Inferred from direct assay Ref.2. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2525 Ref.1
Chain26 – 930905Xanthan lyase
PRO_0000417933

Regions

Region146 – 1483Substrate binding Ref.5
Region313 – 3153Substrate binding Ref.4 Ref.5

Sites

Metal binding5151Calcium Ref.4 Ref.5
Metal binding5161Calcium Ref.4 Ref.5
Metal binding5171Calcium Ref.4 Ref.5
Metal binding6761Calcium Ref.4 Ref.5
Binding site1481Carbohydrate Ref.6
Binding site1481Substrate 1 Ref.4 Ref.5
Binding site2461Substrate 2 Ref.5
Binding site2551Carbohydrate Ref.6
Binding site2551Substrate 1 Ref.4 Ref.5
Binding site3091Carbohydrate Ref.6
Binding site3091Substrate 1 and 2 Ref.4 Ref.5
Binding site3131Carbohydrate Ref.6
Binding site4241Substrate 2 Ref.5
Binding site6121Substrate 1 and 2 Ref.4 Ref.5

Experimental info

Mutagenesis1941N → A: Loss of activity by 60%. Ref.5
Mutagenesis2461H → A: Loss of activity by 60%. Ref.5
Mutagenesis2551Y → F: Loss of activity by 50%. Ref.5
Mutagenesis3131R → A: Reduced catalytic activity. Ref.6
Mutagenesis3151Y → F: Negligible change in catalytic activity. Ref.6
Mutagenesis6121R → A: Increased catalysis rate but decreased affinity with substrate. Ref.6

Secondary structure

1 .................................................................................................................................. 930
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9AQS0 [UniParc].

Last modified June 1, 2001. Version 1.
Checksum: 5E8B69D3E94019C4

FASTA93099,313
        10         20         30         40         50         60 
MLSGILIAAL LMTLWGGWQP DIAHASDEFD ALRIKWATLL TGGPALDPAD SDIAARTDKL 

        70         80         90        100        110        120 
AQDANDYWED MDLSSSRTYI WYALRGNGTS DNVNAVYERL RTMALAATTV GSSLYGNADL 

       130        140        150        160        170        180 
KEDILDALDW LYVNSYNSTR SRSAYNWWHW QLGIPMSLND IAVLLYDDIS AARMATYMDT 

       190        200        210        220        230        240 
IDYFTPSIGL TGANRAWQAI VVGVRAVIVK DAVKLAAARN GLSGTGIFPY ATGGDGFYAD 

       250        260        270        280        290        300 
GSFVQHTTFA YTGGYGSSVL ETTANLMYLL SGSTWSVSDP NQSNVWQWIY EAYRPLLYKG 

       310        320        330        340        350        360 
AMMDMVRGRE ISRSYAQDHA VGHGIVASIV RLAQFAPAPH AAAFKQIAKR VIQEDTFSSF 

       370        380        390        400        410        420 
YGDVSTDTIR LAKAIVDDPS IAPAAAPNLY KQYAAMDRAV LQRPGFALGL ALYSTRISSY 

       430        440        450        460        470        480 
ESINSENGRG WYTGAGATYL YNQDLAQYSE DYWPTVDAYR IPGTTVASGT PIASGTGTSS 

       490        500        510        520        530        540 
WTGGVSLAGQ YGASGMDLSY GAYNLSARKS WFMFDDEIVA LGSGISSTAG IPIETVVDNR 

       550        560        570        580        590        600 
KLNGAGDNAW TANGAALSTG LGVAQTLTGV NWVHLAGNTA DGSDIGYYFP GGATLQTKRE 

       610        620        630        640        650        660 
ARTGTWKQIN NRPATPSTAV TRNYETMWID HGTNPSGASY GYVLLPNKTS AQVGAYAADP 

       670        680        690        700        710        720 
AIEIVVNTSG VQSVKEKTLG LVGANFWTDT TQTADLITSN KKASVMTREI ADERLEASVS 

       730        740        750        760        770        780 
DPTQANNGTI AIELARSAEG YSADPGITVT QLAPTIKFTV NVNGAKGKSF HASFQLGEDT 

       790        800        810        820        830        840 
SGPVDPGEPE LPSVIVDNAD SAGVTRTGTW KTASTQTDRY GANYLHDDNA GKGTKSVTFT 

       850        860        870        880        890        900 
PNLPIAGSYE VYLMWPAHFN REDAVQVDVG HASGTTRTAV DQRSGGGVWH SIGTYEFLAG 

       910        920        930 
SGGSVTIRND ALGSPDGYVV ADAVKFVAVG

« Hide

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AB037178 Genomic DNA. Translation: BAB21059.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalQ9AQS0.
SMRQ9AQS0. Positions 26-777.
ModBaseSearch...

Protein family/group databases

CAZyPL8. Polysaccharide Lyase Family 8.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D1.50.10.100. 1 hit.
2.60.220.10. 1 hit.
2.70.98.10. 1 hit.
InterProIPR008929. 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]
PfamPF02278. Lyase_8. 1 hit.
PF02884. Lyase_8_C. 1 hit.
PF08124. Lyase_8_N. 1 hit.
[Graphical view]
SUPFAMSSF48230. Chondroitin_lyas. 1 hit.
SSF74650. Gal_mut_like. 1 hit.
SSF49863. Lyase_like_C. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ9AQS0.

Entry information

Entry nameXANLY_BACGL
AccessionPrimary (citable) accession number: Q9AQS0
Entry history
Integrated into UniProtKB/Swiss-Prot: June 13, 2012
Last sequence update: June 1, 2001
Last modified: April 3, 2013
This is version 55 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents