Summary: Pectate lyase
Pectate lyase Provide feedback
No Pfam abstract.
Charkowski AO, Alfano JR, Preston G, Yuan J, He SY, Collmer A; , J Bacteriol 1998;180:5211-5217.: The Pseudomonas syringae pv. tomato HrpW protein has domains similar to harpins and pectate lyases and can elicit the plant hypersensitive response and bind to pectate. PUBMED:9748456 EPMC:9748456
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004898
Pectate lyase is responsible for the maceration and soft-rotting of plant tissue. It catalyses the eliminative cleavage of pectate to produce oligosaccharides with 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends. Pectate lyase is an extracellular enzyme and is induced by pectin. It is subject to self-catabolite repression, and has been implicated in plant disease.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]. 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.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||extracellular region (GO:0005576)|
|Molecular function||pectate lyase activity (GO:0030570)|
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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 22 members:Adeno_E1B_55K Autotrns_rpt Beta_helix Chlam_PMP Chondroitinas_B Disaggr_assoc DUF1565 DUF3737 Fil_haemagg Fil_haemagg_2 Glyco_hydro_28 Glyco_hydro_49 Glyco_hydro_80 Glyco_hydro_92 Haemagg_act NosD Pec_lyase_C Pectate_lyase Pectate_lyase_3 Pectinesterase Pertactin PhageP22-tail
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Pfam-B_2273 (release 6.5)|
|Number in seed:||12|
|Number in full:||678|
|Average length of the domain:||205.80 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||67.04 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|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 domain has been found. There are 9 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 seqence.
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