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O31527 (YESX_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 60. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | 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:
Rhamnogalacturonan exolyase yesX
EC=4.2.2.-
Gene names
Name:yesX
Ordered Locus Names:BSU07060
OrganismBacillus subtilis
Taxonomic identifier1423 [NCBI]
Taxonomic lineageBacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length612 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Pectinolytic enzyme that degrades type I rhamnogalacturonan from plant cell walls and releases disaccharide products. Degrades rhamnogalacturonan, polygalacturonic acid and pectic acid. Has very low activity on pectin. Ref.2

Catalytic activity

Exotype eliminative cleavage of alpha-L-rhamnopyranosyl-(1->4)-alpha-D-galactopyranosyluronic acid bonds of rhamnogalacturonan I oligosacharides containing alpha-L-rhamnopyranose at the reducing end and 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end. The products are the disaccharide 2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose and the shortened rhamnogalacturonan oligosaccharide containing one 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end. Ref.2

Cofactor

Divalent metal cations. Has highest activity with manganese, followed by zinc and cobalt. Ref.2

Binds 10 calcium ions By similarity. The calcium may have a structural role. Ref.2

Subunit structure

Monomer.

Subcellular location

Secreted Probable Ref.2.

Induction

Up-regulated by growth on type I rhamnogalacturonan. Ref.2

Sequence similarities

Belongs to the polysaccharide lyase 11 family.

Caution

This enzyme is expected to be secreted, but there is no predicted signal sequence.

Biophysicochemical properties

pH dependence:

Optimum pH is 8.5. Ref.2

Temperature dependence:

Optimum temperature is 60 degrees Celsius.

Ontologies

Keywords
   Biological processCell wall biogenesis/degradation
   Cellular componentSecreted
   DomainRepeat
   LigandCalcium
Metal-binding
   Molecular functionLyase
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological processcellular cell wall organization

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular componentextracellular region

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular functionlyase activity

Inferred from electronic annotation. Source: UniProtKB-KW

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 612612Rhamnogalacturonan exolyase yesX
PRO_0000360213

Regions

Region518 – 5192Substrate binding By similarity

Sites

Metal binding1201Calcium 1 By similarity
Metal binding1251Calcium 2 By similarity
Metal binding1271Calcium 2 By similarity
Metal binding1291Calcium 2 By similarity
Metal binding1311Calcium 2; via carbonyl oxygen
Metal binding1331Calcium 2 By similarity
Metal binding1891Calcium 3 By similarity
Metal binding1911Calcium 3 By similarity
Metal binding1931Calcium 3 By similarity
Metal binding1951Calcium 3; via carbonyl oxygen By similarity
Metal binding1971Calcium 3 By similarity
Metal binding3301Calcium 4 By similarity
Metal binding3361Calcium 5 By similarity
Metal binding3381Calcium 5 By similarity
Metal binding3381Calcium 6 By similarity
Metal binding3401Calcium 5 By similarity
Metal binding3401Calcium 6 By similarity
Metal binding3421Calcium 5; via carbonyl oxygen By similarity
Metal binding3441Calcium 5 By similarity
Metal binding3441Calcium 6 By similarity
Metal binding3531Calcium 6 By similarity
Metal binding3541Calcium 6 By similarity
Metal binding3661Calcium 4 By similarity
Metal binding3681Calcium 4 By similarity
Metal binding3741Calcium 7 By similarity
Metal binding3761Calcium 7; via carbonyl oxygen By similarity
Metal binding3791Calcium 7; via carbonyl oxygen By similarity
Metal binding3811Calcium 7; via carbonyl oxygen By similarity
Metal binding3831Calcium 7 By similarity
Metal binding3891Calcium 4 By similarity
Metal binding4261Calcium 8; via carbonyl oxygen By similarity
Metal binding4291Calcium 8; via carbonyl oxygen By similarity
Metal binding4311Calcium 8; via carbonyl oxygen By similarity
Metal binding4721Calcium 9 By similarity
Metal binding4741Calcium 9 By similarity
Metal binding4761Calcium 9; via carbonyl oxygen By similarity
Metal binding4781Calcium 9 By similarity
Metal binding5271Calcium 10 By similarity
Metal binding5291Calcium 10; via carbonyl oxygen By similarity
Metal binding5311Calcium 10; via carbonyl oxygen By similarity
Metal binding5331Calcium 10; via carbonyl oxygen By similarity
Metal binding5351Calcium 10 By similarity
Metal binding5761Calcium 1; via carbonyl oxygen By similarity
Metal binding5781Calcium 1; via carbonyl oxygen By similarity
Metal binding5801Calcium 1 By similarity
Binding site4191Substrate By similarity
Binding site5791Substrate By similarity

Secondary structure

1 .............................................................................. 612
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O31527 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: E7A320888A608D4B

FASTA61267,690
        10         20         30         40         50         60 
MKPKKRQMEY LTRGLIAVQT EQGVFVSWRF LGTDHETTAF HLYRDGKRIT RDPIAESTNF 

        70         80         90        100        110        120 
LDQNGTADSV YQVAAVNKGR EEKLSKKARV WQENVLEVPL AKPEGGVTPD GKPYTYSAND 

       130        140        150        160        170        180 
ASVGDIDGDG EYEMILKWDP SNSKDNAHDG YTGEVLIDAY KLDGTFLWRI NLGRNIRAGA 

       190        200        210        220        230        240 
HYTQFMVYDL DGDGKAEIAM KTADGTTDGK GHIIGDEQAD FRNEQGRILS GPEYLTVFKG 

       250        260        270        280        290        300 
ETGEALTTVE YEPPRGKLED WGDGYGNRMD RFLAGTAYLD GERPSLVMAR GYYTRTVLVA 

       310        320        330        340        350        360 
YDFRNGRLKK RWVFDSNQPG HEAYAGQGNH SLSVADVDGD GKDEIIYGAM AVDHDGTGLY 

       370        380        390        400        410        420 
STGLGHGDAM HVGDLDPSRK GLEVFQVHED ATKPYGLSLR DAGTGEILWG VHAGTDVGRG 

       430        440        450        460        470        480 
MAAHIDPSYK GSLVWGIDPP GNDGMSYGLF TSKGEKISDK APSSANFAIW WDGDLVRELL 

       490        500        510        520        530        540 
DHDWDGTIGR PKIEKWDAEN GCLKTIFQPA GVLSNNGTKG NPVLQANLFG DWREEVIWRT 

       550        560        570        580        590        600 
EDSSALRIYT TTHLTRHCFY TLMHDPVYRL GIAWQNTAYN QPPHTSFYLG TGMKKPPKPA 

       610 
LYIAGSKAEA PL

« Hide

References

« Hide 'large scale' references
[1]"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. expand/collapse author list , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
Nature 390:249-256(1997) [PubMed: 9384377] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 168.
[2]"Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization."
Ochiai A., Itoh T., Kawamata A., Hashimoto W., Murata K.
Appl. Environ. Microbiol. 73:3803-3813(2007) [PubMed: 17449691] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-6, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBCELLULAR LOCATION, INDUCTION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AL009126 Genomic DNA. Translation: CAB12525.1.
PIRG69797.
RefSeqNP_388587.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2ZUYX-ray1.65A1-612[»]
ProteinModelPortalO31527.
SMRO31527. Positions 3-606.
ModBaseSearch...

Protein family/group databases

CAZyPL11. Polysaccharide Lyase Family 11.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaEBBACT00000000800; EBBACP00000000800; EBBACG00000000798.
GeneID936081.
GenomeReviewsGene locus BSU07060 in contig AL009126_GR.
KEGGbsu:BSU07060.
NMPDRfig|224308.1.peg.706.
PATRIC18973060. VBIBacSub10457_0744.

Organism-specific databases

GenoListBSU07060.

Phylogenomic databases

GeneTreeEBGT00050000006182.
HOGENOMHBG425203.
OMASANFAIW.
PhylomeDBO31527.
ProtClustDBCLSK806638.

Enzyme and pathway databases

BioCycBSUB:BSU07060-MONOMER.
MetaCyc:MONOMER-16402.

Family and domain databases

InterProIPR013517. FG-GAP.
[Graphical view]
PfamPF01839. FG-GAP. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameYESX_BACSU
AccessionPrimary (citable) accession number: O31527
Entry history
Integrated into UniProtKB/Swiss-Prot: January 20, 2009
Last sequence update: January 1, 1998
Last modified: January 25, 2012
This is version 60 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList

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