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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)LengthDescriptionGraphical viewFeature identifierActions
    Sitei41 – 411May be essential to modulate pKa of the D-143 carboxyl group
    Binding sitei88 – 881Substrate
    Sitei88 – 881May be essential to modulate pKa of the D-143 carboxyl group
    Active sitei143 – 1431Proton donor1 Publication

    GO - Molecular functioni

    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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi143 – 1431D → N: Loss of hydrolase activity. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 373372Unsaturated rhamnogalacturonyl hydrolase YteRPRO_0000171597Add
    BLAST

    Proteomic databases

    PaxDbiO34559.

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100016416.

    Structurei

    Secondary structure

    1
    373
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi13 – 2715Combined sources
    Turni30 – 323Combined sources
    Beta strandi33 – 353Combined sources
    Helixi41 – 5717Combined sources
    Helixi60 – 7314Combined sources
    Helixi87 – 893Combined sources
    Helixi91 – 955Combined sources
    Helixi96 – 1038Combined sources
    Helixi106 – 11611Combined sources
    Helixi117 – 1204Combined sources
    Beta strandi139 – 1413Combined sources
    Helixi143 – 15917Combined sources
    Helixi163 – 17917Combined sources
    Turni182 – 1843Combined sources
    Beta strandi189 – 1924Combined sources
    Turni202 – 2043Combined sources
    Helixi212 – 22514Combined sources
    Helixi226 – 2283Combined sources
    Helixi235 – 25117Combined sources
    Turni256 – 2583Combined sources
    Beta strandi262 – 2643Combined sources
    Helixi277 – 29216Combined sources
    Helixi298 – 3003Combined sources
    Helixi301 – 31515Combined sources
    Beta strandi316 – 3183Combined sources
    Beta strandi324 – 3263Combined sources
    Helixi338 – 3425Combined sources
    Beta strandi346 – 3494Combined sources
    Helixi351 – 37020Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1NC5X-ray1.60A1-373[»]
    2D8LX-ray1.70A1-373[»]
    2GH4X-ray1.90A11-373[»]
    ProteinModelPortaliO34559.
    SMRiO34559. Positions 11-373.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO34559.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni40 – 412Substrate binding
    Regioni132 – 1365Substrate binding
    Regioni213 – 2175Substrate binding
    Regioni333 – 3342Substrate binding

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 105 family.Curated

    Phylogenomic databases

    eggNOGiENOG4105F5H. Bacteria.
    COG4225. LUCA.
    HOGENOMiHOG000166045.
    InParanoidiO34559.
    OMAiHQGVFLC.
    OrthoDBiEOG6QK4PM.

    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1NC5X-ray1.60A1-373[»]
    2D8LX-ray1.70A1-373[»]
    2GH4X-ray1.90A11-373[»]
    ProteinModelPortaliO34559.
    SMRiO34559. Positions 11-373.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100016416.

    Protein family/group databases

    CAZyiGH105. Glycoside Hydrolase Family 105.

    Proteomic databases

    PaxDbiO34559.

    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.
    OrthoDBiEOG6QK4PM.

    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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region."
      Lapidus A., Galleron N., Sorokin A., Ehrlich S.D.
      Microbiology 143:3431-3441(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "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.
    3. "A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide."
      Itoh T., Ochiai A., Mikami B., Hashimoto W., Murata K.
      J. Mol. Biol. 360:573-585(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-6, X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, FUNCTION, MUTAGENESIS OF ASP-143, REACTION MECHANISM, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    4. "1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase."
      Zhang R., Minh T., Lezondra L., Korolev S., Moy S.F., Collart F., Joachimiak A.
      Proteins 60:561-565(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
    5. "Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate."
      Itoh T., Ochiai A., Mikami B., Hashimoto W., Murata K.
      Biochem. Biophys. Res. Commun. 347:1021-1029(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 11-373 OF MUTANT ASN-143 IN COMPLEX WITH SUBSTRATE ANALOGS, ACTIVE SITE, MUTAGENESIS OF ASP-143, SUBSTRATE SPECIFICITY.

    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: February 17, 2016
    This is version 95 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.