CAZyme Information: EPrPRT00000020293-p1

Basic Information

• Species: Pythium arrhenomanes
• Lineage: Oomycota; NA; ; Pythiaceae; Pythium; Pythium arrhenomanes
• CAZyme ID: EPrPRT00000020293-p1
• CAZy Family: GH5
• CAZyme Description: Polysaccharide lyase.

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
438		47759.31	4.4184

Genome Property

Genome Version/Assembly ID	Genes	Strain NCBI Taxon ID	Non Protein Coding Genes	Protein Coding Genes
FungiDB-61_ParrhenomanesATCC12531	13857	1223556	52	13805

• Gene Location: location=ParrATCC12531_SC01251:4309-5915(-)

Full Sequence      

MGTYHSSVLTLPELRFLARLSRSTVSTGVPASTLDGTVGAIEAHDIYATVDNTTRSKFYS
GVPFIEDQIHGVSGPKAGVYFVMSPMAYETSIGGPFYRDINNQCTTANELTFYMNSDHTR
TEDYRFGFHGPYALVFTDGPAPISTEVVDFGFYQDLDLQGFYWTQLPPGELAYTSPLMKP
GNYTITVYKKQLAVATASAEVRVAAVRASDIQSTEGRTSQDIASTEVPTSHDITVQFQPN
PDALWTIGEWDGTPSGFLNADKIHEMHPSDDRMTPLLPINFTIGEDDAXXXXHPSDDRMA
PLLPINFTIGQDDAASFPLALFRGFNDPLTIILNLTDTQALDVHTLRIGVTLAQNNGRTT
VTVNDQWSGPAMATAAVKTRGITRGTTTGNYIVYEYTIPSSAFVTGDNKIVLSVTSGNTD
PPEPFLHASVVFDALEFA

Enzyme Prediction     

EC	-	-

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
PL4	162	420	1.5e-45	0.3950617283950617

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
401282	RhgB_N	3.53e-75	1	160	91	251	Rhamnogalacturonan lyase B, N-terminal. Members of this family are found in both fungi, bacteria and wood-eating arthropods. The domain is found at the N-terminus of rhamnogalacturonase B, a member of the polysaccharide lyase family 4. The domain adopts a structure consisting of a beta super-sandwich, with eighteen strands in two beta-sheets. The three domains of the whole protein rhamnogalacturonan lyase (RGL4), are involved in the degradation of rhamnogalacturonan-I, RG-I, an important pectic plant cell-wall polysaccharide. The active-site residues are a lysine at position 169 in UniProtKB:Q00019 and a histidine at 229, Lys169 is likely to be a proton abstractor, His229 a proton donor in the mechanism. The substrate is a disaccharide, and RGL4, in contrast to other rhamnogalacturonan hydrolases, cleaves the alpha-1,4 linkages of RG-I between Rha and GalUA through a beta-elimination resulting in a double bond in the nonreducing GalUA residue, and is thus classified as a polysaccharide lyase (PL).
405384	CBM-like	7.36e-32	243	437	1	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.
199905	RGL4_C	4.73e-31	245	437	1	160	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.
199907	RGL4_N	2.47e-23	9	142	122	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.
405387	fn3_3	3.99e-06	139	205	7	69	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
CCA68112.1|PL4_1	5.17e-89	1	435	112	520
CDJ79831.1|PL4_1	7.13e-83	1	435	115	524
QRW20454.1|PL4_1	1.10e-81	1	436	111	512
QRW23656.1|PL4_1	3.78e-81	1	435	113	519
QRW26043.1|PL4_1	1.33e-78	1	435	71	482

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1NKG_A	1.46e-67	1	436	93	505	Rhamnogalacturonan lyase from Aspergillus aculeatus [Aspergillus aculeatus]
2XHN_A	1.11e-66	1	436	93	505	Rhamnogalacturonan lyase from Aspergillus aculeatus K150A active site mutant [Aspergillus aculeatus],2XHN_B Rhamnogalacturonan lyase from Aspergillus aculeatus K150A active site mutant [Aspergillus aculeatus],3NJV_A Rhamnogalacturonan lyase from Aspergillus aculeatus K150A substrate complex [Aspergillus aculeatus]
3NJX_A	4.28e-66	1	436	93	505	Rhamnogalacturonan Lyase from Aspergillus aculeatus mutant H210A [Aspergillus aculeatus]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
sp|B8NCU7|RGLA_ASPFN	3.13e-72	1	436	113	525	Probable rhamnogalacturonate lyase A OS=Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167) OX=332952 GN=rglA PE=3 SV=1
sp|Q2U0Q1|RGLA_ASPOR	4.39e-72	1	436	113	525	Probable rhamnogalacturonate lyase A OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) OX=510516 GN=rglA PE=3 SV=1
sp|Q00019|RGLA_ASPAC	1.16e-66	1	436	112	524	Rhamnogalacturonate lyase A OS=Aspergillus aculeatus OX=5053 GN=rglA PE=1 SV=1
sp|Q4W9T6|RGLA_ASPFU	6.41e-66	1	436	113	525	Probable rhamnogalacturonate lyase A OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) OX=330879 GN=rglA PE=3 SV=1
sp|B0YEH9|RGLA_ASPFC	6.41e-66	1	436	113	525	Probable rhamnogalacturonate lyase A OS=Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) OX=451804 GN=rglA PE=3 SV=1

SignalP and Lipop Annotations

This protein is predicted as OTHER

Other	SP_Sec_SPI	CS Position
1.000020	0.000025

TMHMM  Annotations     

There is no transmembrane helices in EPrPRT00000020293-p1.