CAZyme Information: VBB81518.1

Basic Information

• Species: Podospora comata
• Lineage: Ascomycota; Sordariomycetes; ; Podosporaceae; Podospora; Podospora comata
• CAZyme ID: VBB81518.1
• CAZy Family: GH47
• CAZyme Description: Putative Glycoside Hydrolase Family 43

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
543		58450.60	7.3213

Genome Property

Genome Version/Assembly ID	Genes	Strain NCBI Taxon ID	Non Protein Coding Genes	Protein Coding Genes
FungiDB-61_PcomataTmat	13100	N/A	2652	10448

• Gene Location: location=LR026968:2719473-2721193(+)

Full Sequence      

MQAAGRQFRSPRYTVCRLLIENISPLKIISTLDLIAATSGCYCTRESAQIAVLDIIHGPQ
ANAHPSLTMKVSALLLTAALASVATADNPIIQTIYSTDPAPLVHNGRVYLYTGHDEPGST
TFVMKDWRVFSSVDMVNWQDHGSPMSLATFSWADANAWAGQTIQRNGKFYWYASMRRRNG
AMAVGVGVSDSPTGPFRDALGRPLVENWGIDPTVWIDDDGQAYMYWGNPGLWYVKLNPDM
VSYSGGINTVTLTTTGFGTRSGNAERPTTYEEGSWIYKRTGKYYMVFAASCCSEHIGYST
GPGPTGPWTYGGVVMPTQGSSFTNHPGVIDYQGSSYFFYHNGALPGGGGYTRSVCVEPFT
YGANGSIPVINMSKDGAPQVGNLNPYVRQEAETIAWESGVQTEPCSEGGMNVLSINNGDY
IKLKGVAFGSGAKSFTARVSSATSGGKIEVRLDSTGGTLVGTCNVPGTGGWQTWTNVNCA
VGGATGTRDLFFRFTGAGGELFRFNWWQFSRIAGLGLYCYQGSLTAVSSSLRGRVAKTVF
ADE

Enzyme Prediction     

EC	3.2.1.37:2	3.2.1.55:2	3.2.1.8:1	3.2.1.8:1	3.2.1.37:1	3.2.1.55:1

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
GH43	88	367	1.1e-113	0.9964028776978417
CBM6	388	510	9.2e-40	0.8768115942028986

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
350130	GH43_Xsa43E-like	9.21e-159	95	368	1	274	Glycosyl hydrolase family 43, including Butyrivibrio proteoclasticus arabinofuranosidase Xsa43E. This glycosyl hydrolase family 43 (GH43) subgroup belongs to the GH43_AXH-like subgroup which includes enzymes that have been characterized with beta-xylosidase (EC 3.2.1.37), alpha-L-arabinofuranosidase (EC 3.2.1.55), alpha-1,2-L-arabinofuranosidase 43A (arabinan-specific; EC 3.2.1.-), endo-alpha-L-arabinanase as well as arabinoxylan arabinofuranohydrolase (AXH) activities. 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. AXHs specifically hydrolyze the glycosidic bond between arabinofuranosyl substituents and xylopyranosyl backbone residues of arabinoxylan. This subgroup includes Cellvibrio japonicus arabinan-specific alpha-1,2-arabinofuranosidase, CjAbf43A, which confers its specificity by a surface cleft that is complementary to the helical backbone of the polysaccharide, and Butyrivibrio proteoclasticus GH43 enzyme Xsa43E, also an arabinofuranosidase, which has been shown to cleave arabinose side chains from short segments of xylan. Several of these enzymes also contain carbohydrate binding modules (CBMs) that bind cellulose or xylan. 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.
350104	GH43_AXH_like	7.45e-113	98	368	2	268	Glycosyl hydrolase family 43 protein, includes arabinoxylan arabinofuranohydrolase, beta-xylosidase, endo-1,4-beta-xylanase, and alpha-L-arabinofuranosidase. This subgroup includes Bacillus subtilis arabinoxylan arabinofuranohydrolase (XynD;BsAXH-m23;BSU18160), Butyrivibrio proteoclasticus alpha-L-arabinofuranosidase (Xsa43E;bpr_I2319), Clostridium stercorarium alpha-L-arabinofuranosidase XylA, and metagenomic beta-xylosidase (EC 3.2.1.37) / alpha-L-arabinofuranosidase (EC 3.2.1.55) CoXyl43. It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. The GH43_AXH-like subgroup includes enzymes that have been characterized with beta-xylosidase, alpha-L-arabinofuranosidase, endo-alpha-L-arabinanase as well as arabinoxylan arabinofuranohydrolase (AXH) activities. 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. AXHs specifically hydrolyze the glycosidic bond between arabinofuranosyl substituents and xylopyranosyl backbone residues of arabinoxylan. Metagenomic beta-xylosidase/alpha-L-arabinofuranosidase CoXyl43 shows synergy with Trichoderma reesei cellulases and promotes plant biomass saccharification by degrading xylo-oligosaccharides, such as xylobiose and xylotriose, into the monosaccharide xylose. Studies show that the hydrolytic activity of CoXyl43 is stimulated in the presence of calcium. Several of these enzymes also contain carbohydrate binding modules (CBMs) that bind cellulose or xylan. 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.
350118	GH43_bXyl-like	3.78e-71	98	367	2	263	Glycosyl hydrolase family 43 protein such as Bacteroides thetaiotaomicron VPI-5482 alpha-L-arabinofuranosidases (BT3675;BT_3675) and (BT3662;BT_3662); includes mostly xylanases. This glycosyl hydrolase family 43 (GH43) subgroup includes enzymes that have been annotated as xylan-digesting beta-xylosidase (EC 3.2.1.37) and xylanase (endo-alpha-L-arabinanase, EC 3.2.1.8) activities, as well the Bacteroides thetaiotaomicron VPI-5482 alpha-L-arabinofuranosidases (EC 3.2.1.55) (BT3675;BT_3675) and (BT3662;BT_3662). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. 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.
350117	GH43_XynD-like	3.03e-70	88	368	1	313	Glycosyl hydrolase family 43 protein such as Bacillus subtilis arabinoxylan arabinofuranohydrolase (XynD;BsAXH-m23;BSU18160). This glycosyl hydrolase family 43 (GH43) subgroup includes characterized Bacillus subtilis arabinoxylan arabinofuranohydrolase (AXH), Caldicellulosiruptor sp. Tok7B.1 beta-1,4-xylanase (EC 3.2.1.8) / alpha-L-arabinosidase (EC 3.2.1.55) XynA, Caldicellulosiruptor sp. Rt69B.1 xylanase C (EC 3.2.1.8) XynC, and Caldicellulosiruptor saccharolyticus beta-xylosidase (EC 3.2.1.37)/ alpha-L-arabinofuranosidase (EC 3.2.1.55) XynF. It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. It belongs to the GH43_AXH-like subgroup which includes enzymes that have been annotated as having beta-xylosidase, alpha-L-arabinofuranosidase and arabinoxylan alpha-L-1,3-arabinofuranohydrolase, xylanase (endo-alpha-L-arabinanase) as well as AXH activities. 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. AXHs specifically hydrolyze the glycosidic bond between arabinofuranosyl substituents and xylopyranosyl backbone residues of arabinoxylan. Bacillus subtilis AXH (BsAXH-m2,3) has been shown to cleave arabinose units from O-2- or O-3-mono-substituted xylose residues and superposition of its structure with known structures of the GH43 exo-acting enzymes, beta-xylosidase and alpha-L-arabinanase, each in complex with their substrate, reveals a different orientation of the sugar backbone. Several of these enzymes also contain carbohydrate binding modules (CBMs) that bind cellulose or xylan. 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.
271150	CBM6_xylanase-like	9.96e-58	390	509	4	123	Carbohydrate Binding Module 6 (CBM6); many are appended to glycoside hydrolase (GH) family 11 and GH43 xylanase domains. This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family domains, including GH3, GH11, and GH43 domains. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. Examples of proteins having CMB6s belonging to this family are Microbispora bispora GghA, a 1,4-beta-D-glucan glucohydrolase (GH3); Clostridium thermocellum xylanase U (GH11), and Penicillium purpurogenum ABF3, a bifunctional alpha-L-arabinofuranosidase/xylobiohydrolase (GH43). GH3 comprises enzymes with activities including beta-glucosidase (hydrolyzes beta-galactosidase) and beta-xylosidase (hydrolyzes 1,4-beta-D-xylosidase). GH11 family comprises enzymes with xylanase (endo-1,4-beta-xylanase) activity which catalyze the hydrolysis of beta-1,4 bonds of xylan, the major component of hemicelluloses, to generate xylooligosaccharides and xylose. GH43 includes beta-xylosidases and beta-xylanases, using aryl-glycosides as substrates. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
VBB81518.1|CBM6|GH43_29	0.0	1	543	1	543
CAP65087.1|CBM6|GH43_29	0.0	4	543	35	578
CDP29823.1|CBM6|GH43_29	0.0	4	543	35	578
QYC44226.1|CBM22|CBM6|GH43_29	1.19e-247	69	510	14	457
QLK01505.1|CBM2|CBM6|GH43_29	3.40e-244	71	509	15	454

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
4NOV_A	9.18e-97	88	367	46	332	Xsa43E, a GH43 family enzyme from Butyrivibrio proteoclasticus [Butyrivibrio proteoclasticus B316]
3QEE_A	3.72e-77	86	376	2	292	The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases [Cellvibrio japonicus Ueda107],3QEE_B The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases [Cellvibrio japonicus Ueda107]
3QEF_A	5.72e-76	86	376	2	292	The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases [Cellvibrio japonicus Ueda107],3QEF_B The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases [Cellvibrio japonicus Ueda107]
3C7E_A	6.27e-75	87	511	13	486	Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from Bacillus subtilis. [Bacillus subtilis],3C7F_A Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from bacillus subtilis in complex with xylotriose. [Bacillus subtilis],3C7H_A Crystal structure of glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from Bacillus subtilis in complex with AXOS-4-0.5. [Bacillus subtilis],3C7O_A Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from Bacillus subtilis in complex with cellotetraose. [Bacillus subtilis]
3C7G_A	6.43e-75	87	511	14	487	Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from Bacillus subtilis in complex with xylotetraose. [Bacillus subtilis]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
sp|Q45071|XYND_BACSU	6.21e-74	87	511	39	512	Arabinoxylan arabinofuranohydrolase OS=Bacillus subtilis (strain 168) OX=224308 GN=xynD PE=1 SV=2
sp|P45796|XYND_PAEPO	4.32e-66	80	510	31	508	Arabinoxylan arabinofuranohydrolase OS=Paenibacillus polymyxa OX=1406 GN=xynD PE=1 SV=1
sp|P49943|XYLB_BACOV	7.35e-37	95	370	13	320	Xylosidase/arabinosidase OS=Bacteroides ovatus OX=28116 GN=xsa PE=2 SV=1
sp|P48791|XYNB_PRERU	9.08e-29	95	370	11	318	Beta-xylosidase OS=Prevotella ruminicola OX=839 GN=xynB PE=3 SV=1
sp|P10478|XYNZ_ACET2	2.96e-12	407	496	322	410	Endo-1,4-beta-xylanase Z OS=Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) OX=203119 GN=xynZ PE=1 SV=3

SignalP and Lipop Annotations

This protein is predicted as OTHER

Other	SP_Sec_SPI	CS Position
1.000056	0.000001

TMHMM  Annotations     

There is no transmembrane helices in VBB81518.1.