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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)DescriptionActionsGraphical viewLength
Metal bindingi153Calcium 11
Metal bindingi158Calcium 21
Metal bindingi160Calcium 21
Metal bindingi162Calcium 21
Metal bindingi164Calcium 2; via carbonyl oxygen1
Metal bindingi166Calcium 21
Metal bindingi222Calcium 31
Metal bindingi224Calcium 31
Metal bindingi226Calcium 31
Metal bindingi228Calcium 3; via carbonyl oxygen1
Metal bindingi230Calcium 31
Metal bindingi363Calcium 41
Metal bindingi369Calcium 51
Metal bindingi371Calcium 51
Metal bindingi371Calcium 61
Metal bindingi373Calcium 51
Metal bindingi373Calcium 61
Metal bindingi375Calcium 5; via carbonyl oxygen1
Metal bindingi377Calcium 51
Metal bindingi377Calcium 61
Metal bindingi386Calcium 61
Metal bindingi387Calcium 61
Metal bindingi399Calcium 41
Metal bindingi401Calcium 41
Metal bindingi407Calcium 71
Metal bindingi409Calcium 7; via carbonyl oxygen1
Metal bindingi412Calcium 7; via carbonyl oxygen1
Metal bindingi414Calcium 7; via carbonyl oxygen1
Metal bindingi416Calcium 71
Metal bindingi422Calcium 41
Binding sitei452Substrate1
Metal bindingi457Calcium 81
Metal bindingi459Calcium 8; via carbonyl oxygen1
Metal bindingi462Calcium 8; via carbonyl oxygen1
Metal bindingi464Calcium 8; via carbonyl oxygen1
Metal bindingi466Calcium 81
Metal bindingi496Calcium 91
Metal bindingi498Calcium 91
Metal bindingi500Calcium 9; via carbonyl oxygen1
Metal bindingi502Calcium 91
Metal bindingi543Calcium 101
Metal bindingi545Calcium 10; via carbonyl oxygen1
Metal bindingi547Calcium 10; via carbonyl oxygen1
Metal bindingi549Calcium 10; via carbonyl oxygen1
Metal bindingi551Calcium 101
Metal bindingi592Calcium 1; via carbonyl oxygen1
Metal bindingi594Calcium 1; via carbonyl oxygen1
Binding sitei595Substrate1
Metal bindingi596Calcium 11

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.

Protein family/group databases

CAZyiPL11. Polysaccharide Lyase Family 11.

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)DescriptionActionsGraphical viewLength
Mutagenesisi363H → A: Strongly reduced catalytic activity. 1 Publication1
Mutagenesisi399H → A: Strongly reduced catalytic activity. 1 Publication1
Mutagenesisi401D → N: Strongly reduced catalytic activity. 1 Publication1
Mutagenesisi422E → Q: Loss of activity. 1 Publication1
Mutagenesisi452R → A: Strongly reduced catalytic activity and reduced affinity for substrate. 1 Publication1
Mutagenesisi535K → A: Strongly reduced catalytic activity and reduced affinity for substrate. 1 Publication1
Mutagenesisi595Y → F: Strongly reduced catalytic activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 371 PublicationAdd BLAST37
ChainiPRO_000036021238 – 620Rhamnogalacturonan endolyase YesWAdd BLAST583

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

1620
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi50 – 54Combined sources5
Beta strandi57 – 61Combined sources5
Beta strandi73 – 78Combined sources6
Beta strandi88 – 95Combined sources8
Beta strandi103 – 110Combined sources8
Beta strandi121 – 132Combined sources12
Beta strandi149 – 157Combined sources9
Beta strandi159 – 164Combined sources6
Beta strandi166 – 173Combined sources8
Beta strandi189 – 193Combined sources5
Beta strandi199 – 204Combined sources6
Turni213 – 215Combined sources3
Beta strandi219 – 221Combined sources3
Beta strandi223 – 228Combined sources6
Beta strandi230 – 235Combined sources6
Beta strandi246 – 248Combined sources3
Beta strandi267 – 272Combined sources6
Turni273 – 275Combined sources3
Beta strandi278 – 283Combined sources6
Helixi291 – 294Combined sources4
Beta strandi297 – 300Combined sources4
Helixi301 – 303Combined sources3
Beta strandi305 – 310Combined sources6
Beta strandi314 – 316Combined sources3
Beta strandi318 – 323Combined sources6
Beta strandi326 – 328Combined sources3
Beta strandi330 – 337Combined sources8
Beta strandi340 – 348Combined sources9
Helixi355 – 357Combined sources3
Beta strandi366 – 368Combined sources3
Beta strandi371 – 375Combined sources5
Beta strandi377 – 380Combined sources4
Beta strandi383 – 385Combined sources3
Beta strandi391 – 394Combined sources4
Beta strandi403 – 406Combined sources4
Beta strandi412 – 414Combined sources3
Beta strandi416 – 420Combined sources5
Beta strandi429 – 434Combined sources6
Turni435 – 437Combined sources3
Beta strandi440 – 444Combined sources5
Beta strandi453 – 456Combined sources4
Beta strandi462 – 464Combined sources3
Beta strandi466 – 469Combined sources4
Beta strandi472 – 474Combined sources3
Beta strandi482 – 484Combined sources3
Beta strandi490 – 493Combined sources4
Beta strandi496 – 500Combined sources5
Beta strandi502 – 505Combined sources4
Beta strandi508 – 513Combined sources6
Turni514 – 517Combined sources4
Beta strandi518 – 524Combined sources7
Helixi533 – 535Combined sources3
Beta strandi539 – 542Combined sources4
Beta strandi545 – 549Combined sources5
Beta strandi551 – 556Combined sources6
Beta strandi559 – 565Combined sources7
Helixi578 – 580Combined sources3
Helixi584 – 590Combined sources7
Beta strandi593 – 595Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiO31526.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni534 – 535Substrate binding2

Sequence similaritiesi

Belongs to the polysaccharide lyase 11 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105CX8. Bacteria.
ENOG410XPAI. LUCA.
HOGENOMiHOG000251614.
InParanoidiO31526.
KOiK18197.
OMAiQRPSLIM.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2Z8RX-ray1.40A/B38-620[»]
2Z8SX-ray2.50A/B38-620[»]
2ZUXX-ray1.32A/B38-620[»]
ProteinModelPortaliO31526.
SMRiO31526.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100003963.

Protein family/group databases

CAZyiPL11. Polysaccharide Lyase Family 11.

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.
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...

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: November 2, 2016
This is version 90 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.