CAZyme Information: MGYG000004721_00736

Basic Information

• Lineage: Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae; Prevotella
• CAZyme ID: MGYG000004721_00736
• CAZy Family: PL4
• CAZyme Description: Rhamnogalacturonate lyase

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
629		69672.72	8.5869

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000004721	2389811	MAG	Denmark	Europe

• Gene Location: Start: 54269; End: 56158 Strand: -

Full Sequence      

MKKLFITLALCFLAAQAAKASDNVTVSLSGRDATMSNGNITIKIGSNGRVSSMTAFGSGN
LLSSSGIYFDLTAKKNVGLSPDKAEIIKQTADYAEVLYSNTKSSPIIHQGYILRKGDNGV
YSYIIVKGTEHSDTTTLREMRVCVRTASTLLNGYVDDRMNGKIPSISEMKVAEKKENTVQ
DATYKLADGTVYTKYNWAQYIVNDSVHGLMNDNYGLWNIACSREWQNGGPMKQELTVHAT
SKSPITIQMLQGEHFGTSAQTYHNGEEKIYGPFYIYANKGTKDEMIADAKKMASEKQKEW
PFQWFSNALYPLDRATVSGCINVTTGQRKDSIQVVLAEPNTDVYAQGKKYIFWALTDQDG
NFTIKNVRKGNYALYAWALAGDNTDELCQKDIDVEDEQMELGTINWTPTCYETKLWQIGS
NNRRSDGFNLSDHLRAYGMWNDVPANLNFTIGESKESTDWYYAQTQNGTWTINFKTDKSY
TGNLYLTASVAGAANKPKVAVALNGNTRATWSTYSDSGIFRSAMLGGKHNLYKLTIPASL
LKTADNKLTLTMSGIKSNGGVMWDCIKLEAGSKVTTGIEQVPETDAVDLVEIYTINGVKM
GTYKTLSDAKHLKGIYIYRKGNKIGKISF

Enzyme Prediction     

No EC number prediction in MGYG000004721_00736.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
PL4	24	566	3.2e-129	0.9963702359346642

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10320	RGL4_N	4.46e-39	26	283	3	262	N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase. The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold; the middle and C-terminal domains are both putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.
cd10317	RGL4_C	1.41e-37	416	569	1	161	C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase. The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.
pfam14683	CBM-like	5.48e-30	415	568	2	157	Polysaccharide lyase family 4, domain III. CBM-like is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll beta-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion.
cd10316	RGL4_M	1.13e-13	313	394	1	81	Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase. The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle domain represented by this model and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.
pfam14686	fn3_3	2.33e-07	334	382	9	59	Polysaccharide lyase family 4, domain II. FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
BBH93641.1	1.17e-136	4	577	19	588
APC39134.1	1.88e-102	85	570	77	563
BAV08848.1	1.05e-99	79	570	104	595
AYH46991.1	1.04e-92	20	568	23	571
AIR69111.1	1.75e-92	20	568	17	565

PDB Hits     

has no PDB hit.

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q8RJP2	5.28e-90	20	568	25	573	Rhamnogalacturonate lyase OS=Dickeya dadantii (strain 3937) OX=198628 GN=rhiE PE=1 SV=1
A5ABH4	7.26e-22	88	550	99	633	Probable rhamnogalacturonate lyase B OS=Aspergillus niger (strain CBS 513.88 / FGSC A1513) OX=425011 GN=rglB PE=3 SV=1
B8N5T6	3.60e-21	78	550	85	633	Probable rhamnogalacturonate lyase B OS=Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167) OX=332952 GN=rglB PE=3 SV=1

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.000293	0.998954	0.000204	0.000184	0.000174	0.000164

TMHMM  Annotations     

There is no transmembrane helices in MGYG000004721_00736.