CAZyme Information: EPrPRT00000020292-p1

Basic Information

• Species: Pythium arrhenomanes
• Lineage: Oomycota; NA; ; Pythiaceae; Pythium; Pythium arrhenomanes
• CAZyme ID: EPrPRT00000020292-p1
• CAZy Family: GH5
• CAZyme Description: Polysaccharide lyase.

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
492		52239.14	7.8952

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_SC01251:6923-8552(-)

Full Sequence      

MPRLFMSVAFALLSAASVSAESFGFKTDTKNWILSSGKGLTITMVRASCDIVSIKYNGQE
LQSDNKGTQLNSGLGNSVTSSITTLSDAAKTIQITCEVPGLTQYYFLRANENALYMGTYH
SSDLKLPELRFLARLSRSTVTTGVPASTLDSTVGAIEAHDIYVKPDNTTRSKFYSGVPFI
EDQIHGVSGPKAGVYFAMSPMAYETSVGAPPISATNFDFFQGLGLKGFVDSTKRGTVSGT
IKDGAGVLDDSAVVVGFSNAAAQYWTTLTSGATKFSSPPMKPGNYMATIYKKQLPVGTTS
VTVAAGKTTTQALAVNFTENADALWRIGDWDGTPDGFLNADKIHKMHPSDARMAAWKPIS
FAAGKDKDASFPMALFRGVNDPLTITFSLKASQAASPHVLKIGVTIAQASGRPTVQVNSK
WTAPMQASVAVQTRGVTRGTTTGNYIIYEYNIPANAFVTGVNEIALGIGSGDTDPPEPFL
AASVVFDALQFE

Enzyme Prediction     

EC	4.2.2.23:4	4.2.2.23:4

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
PL4	205	480	2.3e-91	0.5350701402805611
PL4	21	210	4.1e-48	0.3687374749498998

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
401282	RhgB_N	2.95e-74	23	227	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).
199905	RGL4_C	3.47e-38	325	492	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.
405384	CBM-like	2.61e-31	323	491	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.
199907	RGL4_N	4.92e-23	43	223	43	217	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	8.73e-13	234	310	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
QRW20454.1|PL4_1	1.02e-99	6	490	7	512
CCA68112.1|PL4_1	4.10e-98	16	489	17	520
UQC91653.1|PL4_1	4.95e-98	10	490	12	539
UJO24073.1|PL4_1	2.30e-96	12	490	10	529
BAO51935.1|PL4_1|4.2.2.23	8.11e-96	5	490	3	525

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1NKG_A	5.81e-83	22	490	1	505	Rhamnogalacturonan lyase from Aspergillus aculeatus [Aspergillus aculeatus]
3NJX_A	5.81e-83	22	490	1	505	Rhamnogalacturonan Lyase from Aspergillus aculeatus mutant H210A [Aspergillus aculeatus]
2XHN_A	4.49e-82	22	490	1	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]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
sp|B8NCU7|RGLA_ASPFN	5.37e-93	18	490	17	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	3.26e-91	18	490	17	525	Probable rhamnogalacturonate lyase A OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) OX=510516 GN=rglA PE=3 SV=1
sp|A1C995|RGLA_ASPCL	6.47e-91	18	490	17	525	Probable rhamnogalacturonate lyase A OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1 / QM 1276 / 107) OX=344612 GN=rglA PE=3 SV=1
sp|Q0CVU1|RGLA_ASPTN	4.24e-89	16	485	15	520	Probable rhamnogalacturonate lyase A OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) OX=341663 GN=rglA PE=3 SV=2
sp|P78710|ASD1_NEUCR	2.30e-87	17	490	19	537	Putative rhamnogalacturonase OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) OX=367110 GN=asd-1 PE=2 SV=1

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	CS Position
0.000250	0.999741	CS pos: 20-21. Pr: 0.9800

TMHMM  Annotations     

There is no transmembrane helices in EPrPRT00000020292-p1.