dbCAN-seq: a database of CAZyme sequence and annotation

Basic Information help

Species

Lineage

Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Klebsiella;

CAZyme ID

MGYG000003882_01053

CAZy Family

GH43

CAZyme Description

Beta-xylosidase

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
504	MGYG000003882_87\|CGC1	57306.16	5.5448

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000003882	3911502	MAG	United States	North America

Gene Location

Start: 7706; End: 9220 Strand: -

Enzyme Prediction help

No EC number prediction in MGYG000003882_01053.

CAZyme Signature Domains help

Family	Start	End	Evalue	family coverage
GH43	1	270	1.6e-101	0.8527397260273972

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd09000	GH43_SXA-like	4.34e-144	1	272	41	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	5.19e-114	3	498	65	549	Beta-xylosidase [Carbohydrate transport and metabolism].
cd18617	GH43_XynB-like	2.30e-72	3	269	43	283	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.
cd08989	GH43_XYL-like	2.74e-69	3	264	43	271	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.
pfam04616	Glyco_hydro_43	3.83e-62	3	269	45	280	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 help

Hit ID	Query Start	Query End	Hit Start	Hit End
QAS64624.1	1	504	44	547
QZG73843.1	1	504	44	547
AVE80544.1	1	504	44	547
QTN55926.1	1	504	44	547
QQO68598.1	1	504	44	547

PDB Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1YRZ_A	3.16e-127	1	499	47	527	ChainA, xylan beta-1,4-xylosidase [Halalkalibacterium halodurans C-125],1YRZ_B Chain B, xylan beta-1,4-xylosidase [Halalkalibacterium halodurans C-125]
3C2U_A	1.62e-98	3	499	47	538	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]
1YIF_A	3.09e-97	3	496	47	531	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]
6IFE_A	2.30e-95	3	500	65	553	AGlycoside Hydrolase Family 43 beta-Xylosidase [Bacillus pumilus],6IFE_B A Glycoside Hydrolase Family 43 beta-Xylosidase [Bacillus pumilus]
1Y7B_A	1.24e-91	3	496	48	533	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]

Swiss-Prot Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
P94489	8.52e-97	3	496	47	531	Beta-xylosidase OS=Bacillus subtilis (strain 168) OX=224308 GN=xynB PE=1 SV=2
P07129	1.12e-86	3	495	47	530	Beta-xylosidase OS=Bacillus pumilus OX=1408 GN=xynB PE=1 SV=2
A9ZND1	2.61e-84	3	495	49	532	Xylan 1,3-beta-xylosidase OS=Vibrio sp. OX=678 GN=xloA PE=1 SV=1
P77713	1.22e-81	1	498	45	536	Putative beta-xylosidase OS=Escherichia coli (strain K12) OX=83333 GN=yagH PE=3 SV=1
A7LXU0	4.15e-45	3	499	71	529	Non-reducing end alpha-L-arabinofuranosidase BoGH43B OS=Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153) OX=411476 GN=BACOVA_02656 PE=1 SV=2

SignalP and Lipop Annotations help

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
1.000059	0.000000	0.000000	0.000000	0.000000	0.000000

TMHMM Annotations help

There is no transmembrane helices in MGYG000003882_01053.

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