CAZyme Information: EPrPVT00000019122-p1

Basic Information

• Species: Phytopythium vexans
• Lineage: Oomycota; NA; ; Pythiaceae; Phytopythium; Phytopythium vexans
• CAZyme ID: EPrPVT00000019122-p1
• CAZy Family: GH30
• CAZyme Description: Polysaccharide lyase

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
484		51929.38	9.7646

Genome Property

Genome Version/Assembly ID	Genes	Strain NCBI Taxon ID	Non Protein Coding Genes	Protein Coding Genes
FungiDB-61_PvexansDAOMBR484	11991	1223560	34	11957

• Gene Location: location=PvexDAOMBR484_SC0368:26299-27750(+)

Full Sequence      

MLGNGIVGAAVAALALFSGPSGVDAASFGFTKGTDKYVINSGAGLAITMKQSTCDITSIN
YNGRELQYKSKGTHVNSGLGSAKSTIQTLSDSKKTIQVTCTSSSITQYYFFRPNENVVYM
GTYTKDTSLPELRFLARLDKSVVNAGIKEATMISGMHAIEAEDVYSTSSGQTQSKFYSAI
PFIDDHVHGVKSSAAGVYFVMSDLAYETSSGGPFFRDINNKFDTVNELSFYMNSDHTRTE
SYRYGFHGPYALAFTSGAAPSTSSLDFSFFQSQTMTGFVPNTKRGTVSGTITDSKSVLGS
SDVVVGWSNTDAQYWTKVAAGSKSFTSPKMKPGTYIMTVYKKQLAVGRATVTVSAGSTVK
ATLPVTYTIVSNPIWRIGEWDGTPDGFLNADKIHKMHPSDYRMSAWKSMTFKPGTDSAST
FPMAQFRGANDPITLSFTLSSSQASSARTLRIGISLAQSSARNSITVNGKYTPAVPASVA
VKTR

Enzyme Prediction     

EC	4.2.2.23:4

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
PL4	25	484	1.5e-156	0.9038076152304609

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
401282	RhgB_N	2.98e-120	28	277	1	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).
199907	RGL4_N	2.65e-38	31	263	26	265	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.
199905	RGL4_C	1.19e-29	375	477	1	101	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.
405384	CBM-like	7.14e-26	373	484	1	105	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.
405387	fn3_3	8.69e-16	284	360	2	74	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
QRV98672.1|PL4_1	5.62e-122	26	479	20	455
CCA68112.1|PL4_1	5.52e-121	13	479	9	464
QRW13230.1|PL4_1	1.19e-119	49	478	23	439
QRW20454.1|PL4_1	4.78e-114	26	479	20	455
QRW22552.1|PL4_1	2.66e-112	26	479	17	463

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1NKG_A	1.19e-104	27	478	1	444	Rhamnogalacturonan lyase from Aspergillus aculeatus [Aspergillus aculeatus]
2XHN_A	9.40e-104	27	478	1	444	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	3.72e-103	27	478	1	444	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|Q5AX45|RGLA_EMENI	2.45e-108	26	484	20	470	Rhamnogalacturonate lyase A OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) OX=227321 GN=rglA PE=2 SV=1
sp|B8NCU7|RGLA_ASPFN	5.03e-108	26	468	20	455	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|Q0CVU1|RGLA_ASPTN	7.75e-108	23	478	17	464	Probable rhamnogalacturonate lyase A OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) OX=341663 GN=rglA PE=3 SV=2
sp|B0YEH9|RGLA_ASPFC	1.41e-107	26	478	20	464	Probable rhamnogalacturonate lyase A OS=Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) OX=451804 GN=rglA PE=3 SV=1
sp|Q4W9T6|RGLA_ASPFU	1.41e-107	26	478	20	464	Probable rhamnogalacturonate lyase A OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) OX=330879 GN=rglA PE=3 SV=1

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	CS Position
0.000243	0.999754	CS pos: 25-26. Pr: 0.9741

TMHMM  Annotations     

There is no transmembrane helices in EPrPVT00000019122-p1.