Summary: Pectate lyase
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Pectate lyase Edit Wikipedia article
- Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends
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.
As of late 2007, 32 structures have been solved for this class of enzymes, with PDB accession codes 1AIR, 1BN8, 1EE6, 1GXM, 1GXN, 1GXO, 1JRG, 1JTA, 1O88, 1O8D, 1O8E, 1O8F, 1O8G, 1O8H, 1O8I, 1O8J, 1O8K, 1O8L, 1O8M, 1OOC, 1PCL, 1PE9, 1PLU, 1R76, 1RU4, 1VBL, 2BSP, 2EWE, 2PEC, 2V8I, 2V8J, and 2V8K.
- ALBERSHEIM P, KILLIAS U (1962). "Studies relating to the purification and properties of pectin transeliminase". Arch. Biochem. Biophys. 97: 107â€“15. PMIDÂ 13860094.
- EDSTROM RD, PHAFF HJ (1964). "PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS". J. Biol. Chem. 239: 2403â€“8. PMIDÂ 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. PMIDÂ 14235515.
- Nagel CW and Vaughn RH (1961). "The degradation of oligogalacturonides by the polygalacturonase of Bacillus polymyxa". Arch. Biochem. Biophys. 94: 328.
- Nasuno S, Starr MP (1967). "Polygalacturonic acid trans-eliminase of Xanthomonas campestris". Biochem. J. 104: 178â€“85. PMIDÂ 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: 677â€“89. PMIDÂ 9195887.
Gene Ontology (GO) codes
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Pectate lyase Provide feedback
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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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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|Previous IDs:||pec_lyase; Pec_lyase_C;|
|Number in seed:||5|
|Number in full:||8032|
|Average length of the domain:||188.2 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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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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.