Reviewed, UniProtKB/Swiss-Prot O34559 (URHG2_BACSU)

Names and origin

Protein names

Recommended name:
    Unsaturated rhamnogalacturonyl hydrolase yteR
      Short name=URH
    EC=3.2.1.-

Gene names

Name:	yteR
Ordered Locus Names:	BSU30120

Organism

Bacillus subtilis [Complete proteome] [HAMAP]

Taxonomic identifier

1423 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	373 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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. Ref.3
Subunit structure	Monomer. Ref.3
Subcellular location	Cytoplasm.
Sequence similarities	Belongs to the glycosyl hydrolase 105 family.
biophysicochemical properties	Kinetic parameters: KM=100 µM for unsaturated rhamnogalacturonan disaccharide (at pH 4 and 30 degrees Celsius) pH dependence: Optimum pH is 4.0. Temperature dependence: Optimum temperature is 50 degrees Celsius. It is stable below 50 degrees Celsius.

Ontologies

Keywords
Cellular component	Cytoplasm
Molecular function	Glycosidase Hydrolase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	metabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	hydrolase activity, acting on glycosyl bonds Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.3

Chain

2 – 373

372

Unsaturated rhamnogalacturonyl hydrolase yteR

PRO_0000171597

Regions

Region

40 – 41

2

Substrate binding

Region

133 – 136

4

Substrate binding

Sites

Active site

143

1

Proton donor

Binding site

334

1

Substrate

Site

41

1

May be essential to modulate pKa of the D-143 carboxyl group

Site

88

1

May be essential to modulate pKa of the D-143 carboxyl group

Experimental info

Mutagenesis

143

1

D → N: Loss of hydrolase activity. Ref.3

Secondary structure

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373

Helix Strand Turn

Details...

Helix

13 – 27

15

Turn

30 – 32

3

Beta strand

33 – 35

3

Helix

41 – 57

17

Helix

60 – 73

14

Helix

87 – 89

3

Helix

91 – 95

5

Helix

96 – 103

8

Helix

106 – 116

11

Helix

117 – 120

4

Beta strand

139 – 141

3

Helix

143 – 159

17

Helix

163 – 179

17

Turn

182 – 184

3

Beta strand

189 – 192

4

Turn

202 – 204

3

Helix

212 – 225

14

Helix

226 – 228

3

Helix

235 – 251

17

Turn

256 – 258

3

Beta strand

262 – 264

3

Helix

277 – 292

16

Helix

298 – 300

3

Helix

301 – 315

15

Beta strand

316 – 318

3

Beta strand

324 – 326

3

Helix

338 – 342

5

Beta strand

346 – 349

4

Helix

351 – 370

20

Sequences

	Sequence		Length	Mass (Da)
	O34559-1 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: FC527E1077EB8E86	FASTA	373	42,969
	10 20 30 40 50 60 MGSMDQSIAV KSPLTYAEAL ANTIMNTYTV EELPPANRWH YHQGVFLCGV LRLWEATGEK 70 80 90 100 110 120 RYFEYAKAYA DLLIDDNGNL LFRRDELDAI QAGLILFPLY EQTKDERYVK AAKRLRSLYG 130 140 150 160 170 180 TLNRTSEGGF WHKDGYPYQM WLDGLYMGGP FALKYANLKQ ETELFDQVVL QESLMRKHTK 190 200 210 220 230 240 DAKTGLFYHA WDEAKKMPWA NEETGCSPEF WARSIGWYVM SLADMIEELP KKHPNRHVWK 250 260 270 280 290 300 NTLQDMIKSI CRYQDKETGL WYQIVDKGDR SDNWLESSGS CLYMYAIAKG INKGYLDRAY 310 320 330 340 350 360 ETTLLKAYQG LIQHKTETSE DGAFLVKDIC VGTSAGFYDY YVSRERSTND LHGAGAFILA 370 MTELEPLFRS AGK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 9387221] [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: 9384377] [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: 16781735] [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: 15906318] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AF008220 Genomic DNA. Translation: AAC00272.1.
AL009126 Genomic DNA. Translation: CAB14990.2. Different initiation.

PIR

A69991.

RefSeq

NP_390890.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NC5	X-ray	1.60	A	1-373	[»]
2D8L	X-ray	1.70	A	1-373	[»]
2GH4	X-ray	1.90	A	11-373	[»]

ModBase

Search...

Protein family/group databases

CAZy

GH105. Glycoside Hydrolase Family 105.

Genome annotation databases

GeneID

937273.

GenomeReviews

Gene locus BSU30120 in contig AL009126_GR.

KEGG

bsu:BSU30120.

NMPDR

fig|224308.1.peg.3015.

Organism-specific databases

SubtiList

BG13843. yteR. [Micado]

CMR

Search...

Phylogenomic databases

HOGENOM

O34559.

OMA

O34559. RWHYHQG.

Enzyme and pathway databases

BioCyc

BSUB224308:BSU3007-MON.

Family and domain databases

InterPro

IPR012341. 6hp_glycosidase.
IPR010905. Glyco_hydro_88.
[Graphical view]

Gene3D

G3DSA:1.50.10.10. CelA/Cel48F_cat. 1 hit.

Pfam

PF07470. Glyco_hydro_88. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

URHG2_BACSU

Accession

Primary (citable) accession number: O34559
Secondary accession number(s): Q795R4

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 22, 2005
Last sequence update:	January 1, 1998
Last modified:	June 16, 2009
This is version 53 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)