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Protein

Rhamnogalacturonan endolyase YesW

Gene

yesW

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Pectinolytic enzyme that degrades type I rhamnogalacturonan from plant cell walls and releases oligosaccharide products. Degrades rhamnogalacturonan, polygalacturonic acid, pectic acid and pectin.2 Publications

Catalytic activityi

Endotype eliminative cleavage of L-alpha-rhamnopyranosyl-(1->4)-alpha-D-galactopyranosyluronic acid bonds of rhamnogalacturonan I domains in ramified hairy regions of pectin leaving L-rhamnopyranose at the reducing end and 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end.1 Publication

Cofactori

Ca2+2 Publications, Mn2+2 PublicationsNote: Binds 10 calcium ions. The calcium may have a structural role. Requires calcium or manganese for activity.2 Publications

pH dependencei

Optimum pH is 8.1 Publication

Temperature dependencei

Optimum temperature is 60 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi153 – 1531Calcium 1
Metal bindingi158 – 1581Calcium 2
Metal bindingi160 – 1601Calcium 2
Metal bindingi162 – 1621Calcium 2
Metal bindingi164 – 1641Calcium 2; via carbonyl oxygen
Metal bindingi166 – 1661Calcium 2
Metal bindingi222 – 2221Calcium 3
Metal bindingi224 – 2241Calcium 3
Metal bindingi226 – 2261Calcium 3
Metal bindingi228 – 2281Calcium 3; via carbonyl oxygen
Metal bindingi230 – 2301Calcium 3
Metal bindingi363 – 3631Calcium 4
Metal bindingi369 – 3691Calcium 5
Metal bindingi371 – 3711Calcium 5
Metal bindingi371 – 3711Calcium 6
Metal bindingi373 – 3731Calcium 5
Metal bindingi373 – 3731Calcium 6
Metal bindingi375 – 3751Calcium 5; via carbonyl oxygen
Metal bindingi377 – 3771Calcium 5
Metal bindingi377 – 3771Calcium 6
Metal bindingi386 – 3861Calcium 6
Metal bindingi387 – 3871Calcium 6
Metal bindingi399 – 3991Calcium 4
Metal bindingi401 – 4011Calcium 4
Metal bindingi407 – 4071Calcium 7
Metal bindingi409 – 4091Calcium 7; via carbonyl oxygen
Metal bindingi412 – 4121Calcium 7; via carbonyl oxygen
Metal bindingi414 – 4141Calcium 7; via carbonyl oxygen
Metal bindingi416 – 4161Calcium 7
Metal bindingi422 – 4221Calcium 4
Binding sitei452 – 4521Substrate
Metal bindingi457 – 4571Calcium 8
Metal bindingi459 – 4591Calcium 8; via carbonyl oxygen
Metal bindingi462 – 4621Calcium 8; via carbonyl oxygen
Metal bindingi464 – 4641Calcium 8; via carbonyl oxygen
Metal bindingi466 – 4661Calcium 8
Metal bindingi496 – 4961Calcium 9
Metal bindingi498 – 4981Calcium 9
Metal bindingi500 – 5001Calcium 9; via carbonyl oxygen
Metal bindingi502 – 5021Calcium 9
Metal bindingi543 – 5431Calcium 10
Metal bindingi545 – 5451Calcium 10; via carbonyl oxygen
Metal bindingi547 – 5471Calcium 10; via carbonyl oxygen
Metal bindingi549 – 5491Calcium 10; via carbonyl oxygen
Metal bindingi551 – 5511Calcium 10
Metal bindingi592 – 5921Calcium 1; via carbonyl oxygen
Metal bindingi594 – 5941Calcium 1; via carbonyl oxygen
Binding sitei595 – 5951Substrate
Metal bindingi596 – 5961Calcium 1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Cell wall biogenesis/degradation

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BioCyciBSUB:BSU07050-MONOMER.
MetaCyc:MONOMER-16263.
BRENDAi4.2.2.23. 658.
SABIO-RKO31526.

Names & Taxonomyi

Protein namesi
Recommended name:
Rhamnogalacturonan endolyase YesW (EC:4.2.2.23)
Gene namesi
Name:yesW
Ordered Locus Names:BSU07050
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi363 – 3631H → A: Strongly reduced catalytic activity. 1 Publication
Mutagenesisi399 – 3991H → A: Strongly reduced catalytic activity. 1 Publication
Mutagenesisi401 – 4011D → N: Strongly reduced catalytic activity. 1 Publication
Mutagenesisi422 – 4221E → Q: Loss of activity. 1 Publication
Mutagenesisi452 – 4521R → A: Strongly reduced catalytic activity and reduced affinity for substrate. 1 Publication
Mutagenesisi535 – 5351K → A: Strongly reduced catalytic activity and reduced affinity for substrate. 1 Publication
Mutagenesisi595 – 5951Y → F: Strongly reduced catalytic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 37371 PublicationAdd
BLAST
Chaini38 – 620583Rhamnogalacturonan endolyase YesWPRO_0000360212Add
BLAST

Proteomic databases

PaxDbiO31526.

Expressioni

Inductioni

Up-regulated by growth on type I rhamnogalacturonan.1 Publication

Interactioni

Subunit structurei

Monomer.2 Publications

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100003963.

Structurei

Secondary structure

1
620
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi50 – 545Combined sources
Beta strandi57 – 615Combined sources
Beta strandi73 – 786Combined sources
Beta strandi88 – 958Combined sources
Beta strandi103 – 1108Combined sources
Beta strandi121 – 13212Combined sources
Beta strandi149 – 1579Combined sources
Beta strandi159 – 1646Combined sources
Beta strandi166 – 1738Combined sources
Beta strandi189 – 1935Combined sources
Beta strandi199 – 2046Combined sources
Turni213 – 2153Combined sources
Beta strandi219 – 2213Combined sources
Beta strandi223 – 2286Combined sources
Beta strandi230 – 2356Combined sources
Beta strandi246 – 2483Combined sources
Beta strandi267 – 2726Combined sources
Turni273 – 2753Combined sources
Beta strandi278 – 2836Combined sources
Helixi291 – 2944Combined sources
Beta strandi297 – 3004Combined sources
Helixi301 – 3033Combined sources
Beta strandi305 – 3106Combined sources
Beta strandi314 – 3163Combined sources
Beta strandi318 – 3236Combined sources
Beta strandi326 – 3283Combined sources
Beta strandi330 – 3378Combined sources
Beta strandi340 – 3489Combined sources
Helixi355 – 3573Combined sources
Beta strandi366 – 3683Combined sources
Beta strandi371 – 3755Combined sources
Beta strandi377 – 3804Combined sources
Beta strandi383 – 3853Combined sources
Beta strandi391 – 3944Combined sources
Beta strandi403 – 4064Combined sources
Beta strandi412 – 4143Combined sources
Beta strandi416 – 4205Combined sources
Beta strandi429 – 4346Combined sources
Turni435 – 4373Combined sources
Beta strandi440 – 4445Combined sources
Beta strandi453 – 4564Combined sources
Beta strandi462 – 4643Combined sources
Beta strandi466 – 4694Combined sources
Beta strandi472 – 4743Combined sources
Beta strandi482 – 4843Combined sources
Beta strandi490 – 4934Combined sources
Beta strandi496 – 5005Combined sources
Beta strandi502 – 5054Combined sources
Beta strandi508 – 5136Combined sources
Turni514 – 5174Combined sources
Beta strandi518 – 5247Combined sources
Helixi533 – 5353Combined sources
Beta strandi539 – 5424Combined sources
Beta strandi545 – 5495Combined sources
Beta strandi551 – 5566Combined sources
Beta strandi559 – 5657Combined sources
Helixi578 – 5803Combined sources
Helixi584 – 5907Combined sources
Beta strandi593 – 5953Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z8RX-ray1.40A/B38-620[»]
2Z8SX-ray2.50A/B38-620[»]
2ZUXX-ray1.32A/B38-620[»]
ProteinModelPortaliO31526.
SMRiO31526. Positions 39-620.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO31526.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni534 – 5352Substrate binding

Sequence similaritiesi

Belongs to the polysaccharide lyase 11 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105CX8. Bacteria.
ENOG410XPAI. LUCA.
HOGENOMiHOG000251614.
InParanoidiO31526.
KOiK18197.
OMAiQRPSLIM.
OrthoDBiEOG686NFV.
PhylomeDBiO31526.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
InterProiIPR013783. Ig-like_fold.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

O31526-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRRSCLMIRR RKRMFTAVTL LVLLVMGTSV CPVKAEGAAR QMEALNRGLV
60 70 80 90 100
AVKTDGGIFV SWRFLGTENA SVLFNVYRDG QKLNAAPVKT TNYVDKNGSA
110 120 130 140 150
GSTYTVRAVV NGTEQPASEK ASVWAQPYHS VPLDKPAGGT TPKGESYTYS
160 170 180 190 200
ANDASVGDVD GDGQYELILK WDPSNSKDNS QDGYTGDVLI DAYKLDGTKL
210 220 230 240 250
WRINLGKNIR AGAHYTQFMV YDLDGDGKAE VAMKTADGTK DGTGKVIGNA
260 270 280 290 300
NADYRNEQGR VLSGPEYLTV FQGSTGKELV TANFEPARGN VSDWGDSYGN
310 320 330 340 350
RVDRFLAGIA YLDGQRPSLI MTRGYYAKTM LVAYNFRDGK LSKLWTLDSS
360 370 380 390 400
KSGNEAFAGQ GNHNLSIADV DGDGKDEIIF GSMAVDHDGK GMYSTGLGHG
410 420 430 440 450
DALHTGDLDP GRPGLEVFQV HEDKNAKYGL SFRDAATGKI LWGVYAGKDV
460 470 480 490 500
GRGMAADIDP RYPGQEVWAN GSLYSAKGVK IGSGVPSSTN FGIWWDGDLL
510 520 530 540 550
REQLDSNRID KWDYQNGVSK NMLTASGAAA NNGTKATPTL QADLLGDWRE
560 570 580 590 600
EVVWRTEDSS ALRIYTTTIP TEHRLYTLMH DPVYRLGIAW QNIAYNQPPH
610 620
TSFFLGDGMA EQPKPNMYTP
Length:620
Mass (Da):67,587
Last modified:January 1, 1998 - v1
Checksum:iD4573AF7B3E9358D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL009126 Genomic DNA. Translation: CAB12524.1.
PIRiF69797.
RefSeqiNP_388586.1. NC_000964.3.
WP_010886436.1. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB12524; CAB12524; BSU07050.
GeneIDi938769.
KEGGibsu:BSU07050.
PATRICi18973058. VBIBacSub10457_0743.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL009126 Genomic DNA. Translation: CAB12524.1.
PIRiF69797.
RefSeqiNP_388586.1. NC_000964.3.
WP_010886436.1. NC_000964.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z8RX-ray1.40A/B38-620[»]
2Z8SX-ray2.50A/B38-620[»]
2ZUXX-ray1.32A/B38-620[»]
ProteinModelPortaliO31526.
SMRiO31526. Positions 39-620.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100003963.

Proteomic databases

PaxDbiO31526.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12524; CAB12524; BSU07050.
GeneIDi938769.
KEGGibsu:BSU07050.
PATRICi18973058. VBIBacSub10457_0743.

Phylogenomic databases

eggNOGiENOG4105CX8. Bacteria.
ENOG410XPAI. LUCA.
HOGENOMiHOG000251614.
InParanoidiO31526.
KOiK18197.
OMAiQRPSLIM.
OrthoDBiEOG686NFV.
PhylomeDBiO31526.

Enzyme and pathway databases

BioCyciBSUB:BSU07050-MONOMER.
MetaCyc:MONOMER-16263.
BRENDAi4.2.2.23. 658.
SABIO-RKO31526.

Miscellaneous databases

EvolutionaryTraceiO31526.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
InterProiIPR013783. Ig-like_fold.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  2. "Crystallization and preliminary X-ray analysis of the rhamnogalacturonan lyase YesW from Bacillus subtilis strain 168, a member of polysaccharide lyase family 11."
    Ochiai A., Yamasaki M., Itoh T., Mikami B., Hashimoto W., Murata K.
    Acta Crystallogr. F 62:438-440(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 38-46, CRYSTALLIZATION, COFACTOR, FUNCTION, SUBUNIT.
    Strain: 168.
  3. "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] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBCELLULAR LOCATION, INDUCTION.
  4. "A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller."
    Ochiai A., Itoh T., Maruyama Y., Kawamata A., Mikami B., Hashimoto W., Murata K.
    J. Biol. Chem. 282:37134-37145(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 38-620 IN COMPLEX WITH GALACTURONAN DISACCHARIDE AND CALCIUM IONS, MUTAGENESIS OF HIS-363; HIS-399; ASP-401; GLU-422; ARG-452; LYS-535 AND TYR-595.
    Strain: 168.

Entry informationi

Entry nameiYESW_BACSU
AccessioniPrimary (citable) accession number: O31526
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 20, 2009
Last sequence update: January 1, 1998
Last modified: July 6, 2016
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.