CAZyme Information: MGYG000001490_00428

Basic Information

• Species: Bifidobacterium catenulatum
• Lineage: Bacteria; Actinobacteriota; Actinomycetia; Actinomycetales; Bifidobacteriaceae; Bifidobacterium; Bifidobacterium catenulatum
• CAZyme ID: MGYG000001490_00428
• CAZy Family: GH43
• CAZyme Description: Beta-xylosidase

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
543	MGYG000001490_1|CGC6	62001.65	4.5249

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001490	2079525	Isolate	not provided	not provided

• Gene Location: Start: 503994; End: 505625 Strand: +

Full Sequence      

MKISNPVLTGFHADPSMIRVGDTYYIANSTFEWFPGVRLHESKDLVHWNILPSPLSRSSQ
LDMRGNPSSGGIWAPDLSYADGRFWLIYTDVKVVNGAFKDCTNYLVTAEDIHGPWSEPIR
INGVGFDASLFHDDDGRKYLVQQTWDFREYHHQFDGITLTEFDVDTMKLKPETARTIWDG
TSVKVTEGPHLYKKDGWYYLFAAEGGTVYEHQESVARSRTLDECSFEVMPNGPFIGNFDT
PDTYLQKQGHGALVDTPSGEWYYASLCGRPWRHDTEPAHGTRGWCTLGRETSIQKVEWDE
DGWPRVVGGHGGQRYVDAPKDAIETLAPTTRDEHDEFDSGELGPNWNTLRVPFTDAMGAV
GGGKLALRGQGSLCNLFDLSLVARRWQAFDFDAETKVRFDPKNYMQMAGLTNYYDDLCWS
WAFVTWDEKRHARVIEVAQNDFNQYTSFLKDDAIVVPEEAEAVWLRTKVRTEYYSYEYSF
DGEHFTEIPVRLDAKILSDDYVNQRYGGFFTGAFVGLACVDLSGYDAQAEFDYFDYRELS
DNQ

Enzyme Prediction     

EC	3.2.1.37	3.2.1.55	3.2.1.-

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
GH43	3	304	3.5e-138	0.9965753424657534

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd09000	GH43_SXA-like	0.0	5	306	1	292	Glycosyl hydrolase family 43, such as Selenomonas ruminantium beta-D-xylosidase SXA. This glycosyl hydrolase family 43 (GH43) includes enzymes that have been characterized to mainly have beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37) activity, including Selenomonas ruminantium (Xsa;Sxa;SXA), Bifidobacterium adolescentis ATCC 15703 (XylC;XynB;BAD_0428) and Bacillus sp. KK-1 XylB. They are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds between two xylose units in short xylooligosaccharides. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. These enzymes possess an additional C-terminal beta-sandwich domain that restricts access for substrates to a portion of the active site to form a pocket. The active-site pockets comprise of two subsites, with binding capacity for two monosaccharide moieties and a single route of access for small molecules such as substrate. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.
COG3507	XynB2	0.0	1	539	19	549	Beta-xylosidase [Carbohydrate transport and metabolism].
cd08989	GH43_XYL-like	1.79e-120	5	299	1	272	Glycosyl hydrolase family 43, beta-D-xylosidases and arabinofuranosidases. This glycosyl hydrolase family 43 (GH43) subgroup includes mostly enzymes that have been annotated as having beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37) activity, including Selenomonas ruminantium beta-D-xylosidase SXA. These are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds between two xylose units in short xylooligosaccharides. It also includes various GH43 family GH43 arabinofuranosidases (EC 3.2.1.55) including Humicola insolens alpha-L-arabinofuranosidase AXHd3, Bacteroides ovatus alpha-L-arabinofuranosidase (BoGH43, XynB), and the bifunctional Phanerochaete chrysosporium xylosidase/arabinofuranosidase (Xyl;PcXyl). GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.
cd18617	GH43_XynB-like	8.79e-114	5	304	1	284	Glycosyl hydrolase family 43, such as Bacteroides ovatus alpha-L-arabinofuranosidase (BoGH43, XynB). This glycosyl hydrolase family 43 (GH43) subgroup includes enzymes that have been characterized to have alpha-L-arabinofuranosidase (EC 3.2.1.55) and beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37) activities. Beta-1,4-xylosidases are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds between two xylose units in short xylooligosaccharides. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Also included in this subfamily are Bacteroides ovatus alpha-L-arabinofuranosidases, BoGH43A and BoGH43B, both having a two-domain architecture, consisting of an N-terminal 5-bladed beta-propeller domain harboring the catalytic active site, and a C-terminal beta-sandwich domain. However, despite significant functional overlap between these two enzymes, BoGH43A and BoGH43B share just 41% sequence identity. The latter appears to be significantly less active on the same substrates, suggesting that these paralogs may play subtly different roles during the degradation of xyloglucans from different sources, or may function most optimally at different stages in the catabolism of xyloglucan oligosaccharides (XyGOs), for example before or after hydrolysis of certain side-chain moieties. It also includes Phanerochaete chrysosporium BKM-F-1767 Xyl, a bifunctional xylosidase/arabinofuranosidase. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.
pfam04616	Glyco_hydro_43	2.79e-111	3	304	1	281	Glycosyl hydrolases family 43. The glycosyl hydrolase family 43 contains members that are arabinanases. Arabinanases hydrolyze the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans. The structure of arabinanase Arb43A from Cellvibrio japonicus reveals a five-bladed beta-propeller fold. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
BAR01378.1	0.0	1	543	1	543
BAR03150.1	0.0	1	543	1	543
AVT44870.1	0.0	1	543	1	543
QGM61978.1	0.0	1	543	1	543
BAQ28596.1	0.0	1	543	1	543

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
3C2U_A	5.96e-196	1	539	1	537	Structureof the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane [Selenomonas ruminantium],3C2U_B Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane [Selenomonas ruminantium],3C2U_C Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane [Selenomonas ruminantium],3C2U_D Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane [Selenomonas ruminantium]
1Y7B_A	1.58e-194	3	538	4	534	Beta-d-xylosidase,A Family 43 Glycoside Hydrolase [Clostridium acetobutylicum ATCC 824],1Y7B_B Beta-d-xylosidase, A Family 43 Glycoside Hydrolase [Clostridium acetobutylicum ATCC 824],1Y7B_C Beta-d-xylosidase, A Family 43 Glycoside Hydrolase [Clostridium acetobutylicum ATCC 824],1Y7B_D Beta-d-xylosidase, A Family 43 Glycoside Hydrolase [Clostridium acetobutylicum ATCC 824]
1YI7_A	1.81e-193	3	538	4	534	Beta-d-xylosidase(selenomethionine) XYND from Clostridium Acetobutylicum [Clostridium acetobutylicum ATCC 824],1YI7_B Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum [Clostridium acetobutylicum ATCC 824],1YI7_C Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum [Clostridium acetobutylicum ATCC 824],1YI7_D Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum [Clostridium acetobutylicum ATCC 824]
6IFE_A	1.39e-185	1	541	19	553	AGlycoside Hydrolase Family 43 beta-Xylosidase [Bacillus pumilus],6IFE_B A Glycoside Hydrolase Family 43 beta-Xylosidase [Bacillus pumilus]
1YIF_A	2.84e-185	1	538	1	532	CRYSTALSTRUCTURE OF beta-1,4-xylosidase FROM BACILLUS SUBTILIS, NEW YORK STRUCTURAL GENOMICS CONSORTIUM [Bacillus subtilis],1YIF_B CRYSTAL STRUCTURE OF beta-1,4-xylosidase FROM BACILLUS SUBTILIS, NEW YORK STRUCTURAL GENOMICS CONSORTIUM [Bacillus subtilis],1YIF_C CRYSTAL STRUCTURE OF beta-1,4-xylosidase FROM BACILLUS SUBTILIS, NEW YORK STRUCTURAL GENOMICS CONSORTIUM [Bacillus subtilis],1YIF_D CRYSTAL STRUCTURE OF beta-1,4-xylosidase FROM BACILLUS SUBTILIS, NEW YORK STRUCTURAL GENOMICS CONSORTIUM [Bacillus subtilis]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
P94489	3.85e-185	1	538	1	532	Beta-xylosidase OS=Bacillus subtilis (strain 168) OX=224308 GN=xynB PE=1 SV=2
P77713	6.93e-184	1	539	1	536	Putative beta-xylosidase OS=Escherichia coli (strain K12) OX=83333 GN=yagH PE=3 SV=1
P07129	1.09e-182	1	541	1	535	Beta-xylosidase OS=Bacillus pumilus OX=1408 GN=xynB PE=1 SV=2
A9ZND1	1.37e-123	3	538	5	534	Xylan 1,3-beta-xylosidase OS=Vibrio sp. OX=678 GN=xloA PE=1 SV=1
A7LXT8	5.42e-76	4	537	24	519	Non-reducing end alpha-L-arabinofuranosidase BoGH43A OS=Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153) OX=411476 GN=BACOVA_02654 PE=1 SV=1

SignalP and Lipop Annotations

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
1.000053	0.000012	0.000000	0.000000	0.000000	0.000000

TMHMM  Annotations     

There is no transmembrane helices in MGYG000001490_00428.