Summary: Pectate lyase
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Pectate lyase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / QuickGO|
|Pectate lyase/Amb allergen|
Pectate lyase (EC 188.8.131.52) is an enzyme involved in the maceration and soft rotting of plant tissue. Pectate lyase is responsible for the eliminative cleavage of pectate, yielding oligosaccharides with 4-deoxy-Î±-D-mann-4-enuronosyl groups at their non-reducing ends. The protein is maximally expressed late in pollen development. It has been suggested that the pollen expression of pectate lyase genes might relate to a requirement for pectin degradation during pollen tube growth.
- Eliminative cleavage of (1â†’4)-Î±-D-galacturonan to give oligosaccharides with 4-deoxy-Î±-D-galact-4-enuronosyl groups at their non-reducing ends
The structure and the folding kinetics of one member of this family, pectate lyase C (pelC)1 from Erwinia chrysanthemi has been investigated in some detail,. PelC contains a parallel beta-helix folding motif. The majority of the regular secondary structure is composed of parallel beta-sheets (about 30%). The individual strands of the sheets are connected by unordered loops of varying length. The backbone is then formed by a large helix composed of beta-sheets. There are two disulphide bonds in PelC and 12 proline residues. One of these prolines, Pro220, is involved in a cis peptide bond. The folding mechanism of PelC involves two slow phases that have been attributed to proline isomerization.
Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, synthetic materials, dust, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an Arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation.
The allergens in this family include allergens with the following designations: Amb a 1, Amb a 2, Amb a 3, Cha o 1, Cup a 1, Cry j 1, Jun a 1.
Two of the major allergens in the pollen of short ragweed (Ambrosia artemisiifolia) are Amb a I and Amb a II. The primary structure of Amb a II has been deduced and has been shown to share ~65% sequence identity with the Amb a I multigene family of allergens. Members of the Amb a I/a II family include Tobacco (Nicotiana tabacum, Common tobacco) pectate lyase, which is similar to the deduced amino acid sequences of two pollen-specific pectate lyase genes identified in Lycopersicon esculentum (Tomato); Cry j I, a major allergenic glycoprotein of Cryptomeria japonica (Japanese cedar)â€”the most common pollen allergen in Japan; and P56 and P59, which share sequence similarity with pectate lyases of plant pathogenic bacteria.
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on polysaccharides. The systematic name of this enzyme class is (1->4)-alpha-D-galacturonan lyase. Other names in common use include polygalacturonic transeliminase, pectic acid transeliminase, polygalacturonate lyase, endopectin methyltranseliminase, pectate transeliminase, endogalacturonate transeliminase, pectic acid lyase, pectic lyase, alpha-1,4-D-endopolygalacturonic acid lyase, PGA lyase, PPase-N, endo-alpha-1,4-polygalacturonic acid lyase, polygalacturonic acid lyase, pectin trans-eliminase, and Polygalacturonic acid trans-eliminase. This enzyme participates in pentose and glucuronate interconversions.
- Wing RA, Yamaguchi J, Larabell SK, Ursin VM, McCormick S (1990). "Molecular and genetic characterization of two pollen-expressed genes that have sequence similarity to pectate lyases of the plant pathogen Erwinia" (PDF). Plant Mol. Biol. 14 (1): 17â€“28. doi:10.1007/BF00015651. PMID 1983191.
- Kamen DE, Woody RW (2002). "Folding kinetics of the protein pectate lyase C reveal fast-forming intermediates and slow proline isomerization". Biochemistry. 41 (14): 4713â€“4723. doi:10.1021/bi0115129. PMID 11926834.
- Yoder MD, Keen NT, Jurnak F (1993). "New domain motif: the structure of pectate lyase C, a secreted plant virulence factor". Science. 260 (5113): 1503â€“1507. doi:10.1126/science.8502994. PMID 8502994.
- WHO/IUIS Allergen Nomenclature Subcommittee (King TP, Hoffmann D, Loewenstein H, Marsh DG, Platts-Mills TAE, Bull TW). World Health Organ. 72:797â€“806 (1994).
- King TP, Rogers BL, Morgenstern JP, Griffith IJ, Yu XB, Counsell CM, Brauer AW, Garman RD, Kuo MC (1991). "Complete sequence of the allergen Amb Î± II. Recombinant expression and reactivity with T cells from ragweed allergic patients". J. Immunol. 147 (8): 2547â€“2552. PMID 1717566.
- Rogers HJ, Harvey A, Lonsdale DM (1992). "Isolation and characterization of a tobacco gene with homology to pectate lyase which is specifically expressed during microsporogenesis". Plant Mol. Biol. 20 (3): 493â€“502. doi:10.1007/BF00040608. PMID 1421152.
- Kojima K, Ogawa H, Hijikata A, Matsumoto I (1994). "Antigenicity of the oligosaccharide moiety of the Japanese cedar (Cryptomeria japonica pollen allergen, Cry j I". Int. Arch. Allergy Immunol. 105 (2): 198â€“202. doi:10.1159/000236826. PMID 7920021.
- Albersheim P, Killias U (1962). "Studies relating to the purification and properties of pectin transeliminase". Arch. Biochem. Biophys. 97 (1): 107â€“15. doi:10.1016/0003-9861(62)90050-4. PMID 13860094.
- Edstrom RD, Phaff HJ (1964). "Purification and Certain Properties of Pectin trans-Eliminase from Aspergillus fonsecaeus". J. Biol. Chem. 239: 2403â€“8. PMID 14235514.
- Edstrom RD, Phaff HJ (1964). "Eliminative Cleavage of Pectin and of Oligogalacturonide Methyl Esters by Pectin trans-Eliminase". J. Biol. Chem. 239: 2409â€“15. PMID 14235515.
- Nagel CW, Vaughn RH (1961). "The degradation of oligogalacturonides by the polygalacturonase of Bacillus polymyxa". Arch. Biochem. Biophys. 94 (2): 328â€“32. doi:10.1016/0003-9861(61)90047-9. PMID 13727438.
- Nasuno S, Starr MP (1967). "Polygalacturonic acid trans-eliminase of Xanthomonas campestris". Biochem. J. 104 (1): 178â€“85. doi:10.1042/bj1040178. PMC 1270559. PMID 6035509.
- Pickersgill R, Jenkins J (1997). "Two crystal structures of pectin lyase A from Aspergillus reveal a pH-driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases". Structure. 5 (5): 677â€“89. doi:10.1016/S0969-2126(97)00222-0. PMID 9195887.
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This enzyme forms a right handed beta helix structure. Pectate lyase is an enzyme involved in the maceration and soft rotting of plant tissue.
Internal database links
|SCOOP:||Beta_helix Glyco_hydro_28 NosD|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002022
Pectate lyase EC is an enzyme involved in the maceration and soft rotting of plant tissue. Pectate lyase is responsible for the eliminative cleavage of pectate, yielding oligosaccharides with 4-deoxy-alpha-D-mann-4-enuronosyl groups at their non-reducing ends. The protein is maximally expressed late in pollen development. It has been suggested that the pollen expression of pectate lyase genes might relate to a requirement for pectin degradation during pollen tube growth [ PUBMED:1983191 ].
The structure and the folding kinetics of one member of this family, pectate lyase C (pelC)1 from Erwinia chrysanthemi has been investigated in some detail [ PUBMED:11926834 , PUBMED:8502994 ]. PelC contains a parallel beta-helix folding motif. The majority of the regular secondary structure is composed of parallel beta-sheets (about 30%). The individual strands of the sheets are connected by unordered loops of varying length. The backbone is then formed by a large helix composed of beta-sheets. There are two disulphide bonds in pelC and 12 proline residues. One of these prolines, Pro220, is involved in a cis peptide bond. he folding mechanism of pelC involves two slow phases that have been attributed to proline isomerization.
Some of the proteins in this family are allergens [ PUBMED:25978036 ].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This superfamily all contain a right handed beta helix similar to that first found in pectate lyase .
The clan contains the following 41 members:AC_1 Adeno_E1B_55K AIDA B_solenoid_dext B_solenoid_ydck Bactofilin Beta_helix Beta_helix_2 Beta_helix_3 Chlam_PMP Chondroitinas_B Cthe_2159 Disaggr_assoc DUF1565 DUF2154 DUF2807 DUF3737 DUF4097 DUF4957 DUF5649 End_N_terminal FapA Fil_haemagg Fil_haemagg_2 Glyco_hydro_28 Glyco_hydro_49 Glyco_hydro_92 IPU_b_solenoid MinC_C NosD PATR Pectate_lyase Pectate_lyase_3 Pectate_lyase_4 Pectinesterase Pertactin Phage_spike_2 PhageP22-tail Toast_rack_N TPS VacA
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Key: available, not generated, — not available.
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|Previous IDs:||pec_lyase; Pec_lyase_C;|
|Number in seed:||5|
|Number in full:||8032|
|Average length of the domain:||188.20 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||43.34 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||22|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Pectate_lyase_4 domain has been found. There are 57 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.