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Protein

Unsaturated rhamnogalacturonyl hydrolase YteR

Gene

yteR

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

Functioni

Catalyzes the hydrolysis of unsaturated rhamnogalacturonan disaccharide to yield unsaturated D-galacturonic acid and L-rhamnose. It cannot act on unsaturated glucuronyl hydrolase (UGL) substrates containing unsaturated D-glucuronic acid at the non-reducing terminus, although the active pockets of YesR and UGL are very similar.1 Publication

Catalytic activityi

2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O = 5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose.

Kineticsi

  1. KM=100 µM for unsaturated rhamnogalacturonan disaccharide (at pH 4 and 30 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 4.0.1 Publication

    Temperature dependencei

    Optimum temperature is 50 degrees Celsius. It is stable below 50 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sitei41May be essential to modulate pKa of the D-143 carboxyl group1
    Binding sitei88Substrate1
    Sitei88May be essential to modulate pKa of the D-143 carboxyl group1
    Active sitei143Proton donor1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Enzyme and pathway databases

    BioCyciBSUB:BSU30120-MONOMER.
    BRENDAi3.2.1.172. 658.

    Protein family/group databases

    CAZyiGH105. Glycoside Hydrolase Family 105.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Unsaturated rhamnogalacturonyl hydrolase YteR (EC:3.2.1.172)
    Short name:
    URH
    Gene namesi
    Name:yteR
    Ordered Locus Names:BSU30120
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi143D → N: Loss of hydrolase activity. 2 Publications1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00001715972 – 373Unsaturated rhamnogalacturonyl hydrolase YteRAdd BLAST372

    Proteomic databases

    PaxDbiO34559.
    PRIDEiO34559.

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100016416.

    Structurei

    Secondary structure

    1373
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi13 – 27Combined sources15
    Turni30 – 32Combined sources3
    Beta strandi33 – 35Combined sources3
    Helixi41 – 57Combined sources17
    Helixi60 – 73Combined sources14
    Helixi87 – 89Combined sources3
    Helixi91 – 95Combined sources5
    Helixi96 – 103Combined sources8
    Helixi106 – 116Combined sources11
    Helixi117 – 120Combined sources4
    Beta strandi139 – 141Combined sources3
    Helixi143 – 159Combined sources17
    Helixi163 – 179Combined sources17
    Turni182 – 184Combined sources3
    Beta strandi189 – 192Combined sources4
    Turni202 – 204Combined sources3
    Helixi212 – 225Combined sources14
    Helixi226 – 228Combined sources3
    Helixi235 – 251Combined sources17
    Turni256 – 258Combined sources3
    Beta strandi262 – 264Combined sources3
    Helixi277 – 292Combined sources16
    Helixi298 – 300Combined sources3
    Helixi301 – 315Combined sources15
    Beta strandi316 – 318Combined sources3
    Beta strandi324 – 326Combined sources3
    Helixi338 – 342Combined sources5
    Beta strandi346 – 349Combined sources4
    Helixi351 – 370Combined sources20

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1NC5X-ray1.60A1-373[»]
    2D8LX-ray1.70A1-373[»]
    2GH4X-ray1.90A11-373[»]
    ProteinModelPortaliO34559.
    SMRiO34559.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO34559.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni40 – 41Substrate binding2
    Regioni132 – 136Substrate binding5
    Regioni213 – 217Substrate binding5
    Regioni333 – 334Substrate binding2

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 105 family.Curated

    Phylogenomic databases

    eggNOGiENOG4105F5H. Bacteria.
    COG4225. LUCA.
    HOGENOMiHOG000166045.
    InParanoidiO34559.
    OMAiHQGVFLC.

    Family and domain databases

    Gene3Di1.50.10.10. 1 hit.
    InterProiIPR008928. 6-hairpin_glycosidase-like.
    IPR012341. 6hp_glycosidase.
    IPR010905. Glyco_hydro_88.
    [Graphical view]
    PfamiPF07470. Glyco_hydro_88. 1 hit.
    [Graphical view]
    SUPFAMiSSF48208. SSF48208. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    O34559-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MGSMDQSIAV KSPLTYAEAL ANTIMNTYTV EELPPANRWH YHQGVFLCGV
    60 70 80 90 100
    LRLWEATGEK RYFEYAKAYA DLLIDDNGNL LFRRDELDAI QAGLILFPLY
    110 120 130 140 150
    EQTKDERYVK AAKRLRSLYG TLNRTSEGGF WHKDGYPYQM WLDGLYMGGP
    160 170 180 190 200
    FALKYANLKQ ETELFDQVVL QESLMRKHTK DAKTGLFYHA WDEAKKMPWA
    210 220 230 240 250
    NEETGCSPEF WARSIGWYVM SLADMIEELP KKHPNRHVWK NTLQDMIKSI
    260 270 280 290 300
    CRYQDKETGL WYQIVDKGDR SDNWLESSGS CLYMYAIAKG INKGYLDRAY
    310 320 330 340 350
    ETTLLKAYQG LIQHKTETSE DGAFLVKDIC VGTSAGFYDY YVSRERSTND
    360 370
    LHGAGAFILA MTELEPLFRS AGK
    Length:373
    Mass (Da):42,969
    Last modified:January 1, 1998 - v1
    Checksum:iFC527E1077EB8E86
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF008220 Genomic DNA. Translation: AAC00272.1.
    AL009126 Genomic DNA. Translation: CAB14990.3.
    PIRiA69991.

    Genome annotation databases

    EnsemblBacteriaiCAB14990; CAB14990; BSU30120.
    PATRICi18977928. VBIBacSub10457_3152.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF008220 Genomic DNA. Translation: AAC00272.1.
    AL009126 Genomic DNA. Translation: CAB14990.3.
    PIRiA69991.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1NC5X-ray1.60A1-373[»]
    2D8LX-ray1.70A1-373[»]
    2GH4X-ray1.90A11-373[»]
    ProteinModelPortaliO34559.
    SMRiO34559.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100016416.

    Protein family/group databases

    CAZyiGH105. Glycoside Hydrolase Family 105.

    Proteomic databases

    PaxDbiO34559.
    PRIDEiO34559.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB14990; CAB14990; BSU30120.
    PATRICi18977928. VBIBacSub10457_3152.

    Phylogenomic databases

    eggNOGiENOG4105F5H. Bacteria.
    COG4225. LUCA.
    HOGENOMiHOG000166045.
    InParanoidiO34559.
    OMAiHQGVFLC.

    Enzyme and pathway databases

    BioCyciBSUB:BSU30120-MONOMER.
    BRENDAi3.2.1.172. 658.

    Miscellaneous databases

    EvolutionaryTraceiO34559.

    Family and domain databases

    Gene3Di1.50.10.10. 1 hit.
    InterProiIPR008928. 6-hairpin_glycosidase-like.
    IPR012341. 6hp_glycosidase.
    IPR010905. Glyco_hydro_88.
    [Graphical view]
    PfamiPF07470. Glyco_hydro_88. 1 hit.
    [Graphical view]
    SUPFAMiSSF48208. SSF48208. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiURHG2_BACSU
    AccessioniPrimary (citable) accession number: O34559
    Secondary accession number(s): Q795R4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 22, 2005
    Last sequence update: January 1, 1998
    Last modified: November 2, 2016
    This is version 99 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. Glycosyl hydrolases
      Classification of glycosyl hydrolase families and list of entries
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.