CAZyme Information: QRD05666.1

Basic Information

• Species: Parastagonospora nodorum
• Lineage: Ascomycota; Dothideomycetes; ; Phaeosphaeriaceae; Parastagonospora; Parastagonospora nodorum
• CAZyme ID: QRD05666.1
• CAZy Family: GT1
• CAZyme Description: rhamnogalacturonate lyase

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
527	CP069041|CGC5	55973.52	6.5869

Genome Property

Genome Version/Assembly ID	Genes	Strain NCBI Taxon ID	Non Protein Coding Genes	Protein Coding Genes
FungiDB-61_PnodorumSN15	17580	321614	132	17448

• Gene Location: location=CP069041:358783-360529(+)

Full Sequence      

MHLITSVATVLSIGQGVSAAFGLTSTTTGYKVDTDGGLVFEINKSTGDLTSLNYNGVEYQ
GTVKASGINSGLGSSTVTAETINGFIKITAKSSSLPVTHYYIAKPQEASIYMATNNQGEV
DPGELRFLARLQVSEVPTGVHGNVGDVRGCTAIEGKDTFRCSDGHTACKMYTSDRFIDDK
VHCVSGSKAQVCMSMPGLAYETSSGGPFMRDINSQTTDPDQELYFYMNSGHVRTEAWRSG
LKGPYAITFQPAGASPPSAPDTSFFGSLKIDGYVGESGRGSVTGKATGVDSKFETVLHWY
NDAAQYWTKASGGNYKSPAMKAGTYNMKLYKGEFVVATDTVTVTAGQTASKDIASKEVSP
AVIWRIGEFDGQPFELKNGDKITRMHPSDVRMSSWAGSYTVGTSKASDFPMALWAKQNTA
ANVTFELTSAQVKAHVLRVGTTLSFKGGRPSVKIGSWTGTDPGAPTLIDSRGVTRGAYRG
FGEVYTWTVPASAFQAGANTLTMGVSGSGDAEWLSANYIVDAVELQD

Enzyme Prediction     

EC	4.2.2.23:4

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
PL4	19	515	2.6e-186	0.9919839679358717

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
401282	RhgB_N	1.81e-130	21	272	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	7.16e-53	364	526	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	4.12e-51	362	525	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	2.83e-42	21	254	1	261	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	9.48e-13	278	334	1	56	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
QRD05666.1|PL4_1	0.0	1	527	1	527
EGX51477.1|CBM1|PL4_1	3.04e-206	19	526	18	522
QDS74173.1|PL4_1	2.99e-196	17	527	17	528
EAA61387.1|PL4_1|4.2.2.23	2.44e-162	18	525	19	525
ABF50880.1|PL4_1|4.2.2.23	2.44e-162	18	525	19	525

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1NKG_A	1.19e-153	20	525	1	506	Rhamnogalacturonan lyase from Aspergillus aculeatus [Aspergillus aculeatus]
2XHN_A	9.55e-153	20	525	1	506	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	3.83e-152	20	525	1	506	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	4.34e-163	18	525	19	525	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|Q0CVU1|RGLA_ASPTN	1.55e-156	18	519	19	520	Probable rhamnogalacturonate lyase A OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) OX=341663 GN=rglA PE=3 SV=2
sp|B0YEH9|RGLA_ASPFC	1.98e-156	19	525	20	526	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	1.98e-156	19	525	20	526	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|A1C995|RGLA_ASPCL	1.28e-154	19	525	20	526	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

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	CS Position
0.000252	0.999737	CS pos: 19-20. Pr: 0.9726

TMHMM  Annotations     

There is no transmembrane helices in QRD05666.1.