URHG2_BACSU
ID URHG2_BACSU Reviewed; 373 AA.
AC O34559; Q795R4;
DT 22-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Unsaturated rhamnogalacturonyl hydrolase YteR;
DE Short=URH;
DE EC=3.2.1.172;
GN Name=yteR; OrderedLocusNames=BSU30120;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9387221; DOI=10.1099/00221287-143-11-3431;
RA Lapidus A., Galleron N., Sorokin A., Ehrlich S.D.;
RT "Sequencing and functional annotation of the Bacillus subtilis genes in the
RT 200 kb rrnB-dnaB region.";
RL Microbiology 143:3431-3441(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP PROTEIN SEQUENCE OF 2-6, X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX
RP WITH SUBSTRATE ANALOGS, FUNCTION, MUTAGENESIS OF ASP-143, REACTION
RP MECHANISM, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=16781735; DOI=10.1016/j.jmb.2006.04.047;
RA Itoh T., Ochiai A., Mikami B., Hashimoto W., Murata K.;
RT "A novel glycoside hydrolase family 105: the structure of family 105
RT unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in
RT comparison with family 88 enzyme complexed with the disaccharide.";
RL J. Mol. Biol. 360:573-585(2006).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
RX PubMed=15906318; DOI=10.1002/prot.20410;
RA Zhang R., Minh T., Lezondra L., Korolev S., Moy S.F., Collart F.,
RA Joachimiak A.;
RT "1.6 A crystal structure of YteR protein from Bacillus subtilis, a
RT predicted lyase.";
RL Proteins 60:561-565(2005).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 11-373 OF MUTANT ASN-143 IN
RP COMPLEX WITH SUBSTRATE ANALOGS, ACTIVE SITE, MUTAGENESIS OF ASP-143, AND
RP SUBSTRATE SPECIFICITY.
RX PubMed=16870154; DOI=10.1016/j.bbrc.2006.07.034;
RA Itoh T., Ochiai A., Mikami B., Hashimoto W., Murata K.;
RT "Structure of unsaturated rhamnogalacturonyl hydrolase complexed with
RT substrate.";
RL Biochem. Biophys. Res. Commun. 347:1021-1029(2006).
CC -!- FUNCTION: Catalyzes the hydrolysis of unsaturated rhamnogalacturonan
CC disaccharide to yield unsaturated D-galacturonic acid and L-rhamnose.
CC It cannot act on unsaturated glucuronyl hydrolase (UGL) substrates
CC containing unsaturated D-glucuronic acid at the non-reducing terminus,
CC although the active pockets of YesR and UGL are very similar.
CC {ECO:0000269|PubMed:16781735}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-
CC rhamnose + H2O = 5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose;
CC Xref=Rhea:RHEA:30927, ChEBI:CHEBI:15377, ChEBI:CHEBI:17117,
CC ChEBI:CHEBI:62346, ChEBI:CHEBI:62478; EC=3.2.1.172;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=100 uM for unsaturated rhamnogalacturonan disaccharide (at pH 4
CC and 30 degrees Celsius) {ECO:0000269|PubMed:16781735};
CC pH dependence:
CC Optimum pH is 4.0. {ECO:0000269|PubMed:16781735};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius. It is stable below 50
CC degrees Celsius. {ECO:0000269|PubMed:16781735};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:16781735,
CC ECO:0000269|PubMed:16870154}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 105 family.
CC {ECO:0000305}.
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DR EMBL; AF008220; AAC00272.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB14990.3; -; Genomic_DNA.
DR PIR; A69991; A69991.
DR RefSeq; NP_390890.2; NC_000964.3.
DR PDB; 1NC5; X-ray; 1.60 A; A=1-373.
DR PDB; 2D8L; X-ray; 1.70 A; A=1-373.
DR PDB; 2GH4; X-ray; 1.90 A; A=11-373.
DR PDBsum; 1NC5; -.
DR PDBsum; 2D8L; -.
DR PDBsum; 2GH4; -.
DR AlphaFoldDB; O34559; -.
DR SMR; O34559; -.
DR STRING; 224308.BSU30120; -.
DR CAZy; GH105; Glycoside Hydrolase Family 105.
DR PaxDb; O34559; -.
DR PRIDE; O34559; -.
DR EnsemblBacteria; CAB14990; CAB14990; BSU_30120.
DR GeneID; 937273; -.
DR KEGG; bsu:BSU30120; -.
DR eggNOG; COG4225; Bacteria.
DR InParanoid; O34559; -.
DR OMA; HQGVFLC; -.
DR BioCyc; BSUB:BSU30120-MON; -.
DR BRENDA; 3.2.1.172; 658.
DR EvolutionaryTrace; O34559; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0102211; F:unsaturated rhamnogalacturonyl hydrolase activity; IEA:UniProtKB-EC.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:InterPro.
DR GO; GO:1901575; P:organic substance catabolic process; IEA:UniProt.
DR Gene3D; 1.50.10.10; -; 1.
DR InterPro; IPR008928; 6-hairpin_glycosidase_sf.
DR InterPro; IPR012341; 6hp_glycosidase-like_sf.
DR InterPro; IPR010905; Glyco_hydro_88.
DR Pfam; PF07470; Glyco_hydro_88; 1.
DR SUPFAM; SSF48208; SSF48208; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Glycosidase; Hydrolase;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:16781735"
FT CHAIN 2..373
FT /note="Unsaturated rhamnogalacturonyl hydrolase YteR"
FT /id="PRO_0000171597"
FT ACT_SITE 143
FT /note="Proton donor"
FT /evidence="ECO:0000269|PubMed:16870154"
FT BINDING 40..41
FT /ligand="substrate"
FT BINDING 88
FT /ligand="substrate"
FT BINDING 132..136
FT /ligand="substrate"
FT BINDING 213..217
FT /ligand="substrate"
FT BINDING 333..334
FT /ligand="substrate"
FT SITE 41
FT /note="May be essential to modulate pKa of the D-143
FT carboxyl group"
FT SITE 88
FT /note="May be essential to modulate pKa of the D-143
FT carboxyl group"
FT MUTAGEN 143
FT /note="D->N: Loss of hydrolase activity."
FT /evidence="ECO:0000269|PubMed:16781735,
FT ECO:0000269|PubMed:16870154"
FT HELIX 13..27
FT /evidence="ECO:0007829|PDB:1NC5"
FT TURN 30..32
FT /evidence="ECO:0007829|PDB:1NC5"
FT STRAND 33..35
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 41..57
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 60..73
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 91..95
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 96..103
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 106..116
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 117..120
FT /evidence="ECO:0007829|PDB:1NC5"
FT STRAND 139..141
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 143..159
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 163..179
FT /evidence="ECO:0007829|PDB:1NC5"
FT TURN 182..184
FT /evidence="ECO:0007829|PDB:1NC5"
FT STRAND 189..192
FT /evidence="ECO:0007829|PDB:1NC5"
FT TURN 202..204
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 212..225
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 226..228
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 235..251
FT /evidence="ECO:0007829|PDB:1NC5"
FT TURN 256..258
FT /evidence="ECO:0007829|PDB:1NC5"
FT STRAND 262..264
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 277..292
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 298..300
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 301..315
FT /evidence="ECO:0007829|PDB:1NC5"
FT STRAND 316..318
FT /evidence="ECO:0007829|PDB:1NC5"
FT STRAND 324..326
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 338..342
FT /evidence="ECO:0007829|PDB:1NC5"
FT STRAND 346..349
FT /evidence="ECO:0007829|PDB:1NC5"
FT HELIX 351..370
FT /evidence="ECO:0007829|PDB:1NC5"
SQ SEQUENCE 373 AA; 42969 MW; FC527E1077EB8E86 CRC64;
MGSMDQSIAV KSPLTYAEAL ANTIMNTYTV EELPPANRWH YHQGVFLCGV LRLWEATGEK
RYFEYAKAYA DLLIDDNGNL LFRRDELDAI QAGLILFPLY EQTKDERYVK AAKRLRSLYG
TLNRTSEGGF WHKDGYPYQM WLDGLYMGGP FALKYANLKQ ETELFDQVVL QESLMRKHTK
DAKTGLFYHA WDEAKKMPWA NEETGCSPEF WARSIGWYVM SLADMIEELP KKHPNRHVWK
NTLQDMIKSI CRYQDKETGL WYQIVDKGDR SDNWLESSGS CLYMYAIAKG INKGYLDRAY
ETTLLKAYQG LIQHKTETSE DGAFLVKDIC VGTSAGFYDY YVSRERSTND LHGAGAFILA
MTELEPLFRS AGK
