Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
57  structures 1234  species 0  interactions 7667  sequences 223  architectures

Family: Pectate_lyase_4 (PF00544)

Summary: Pectate lyase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Pectate lyase". More...

Pectate lyase Edit Wikipedia article

pectate lyase
Identifiers
EC number4.2.2.2
CAS number9015-75-2
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
Pectate lyase/Amb allergen
Identifiers
SymbolAmb_allergen
PfamPF00544
InterProIPR002022
SMARTSM00656
Membranome596

Pectate lyase (EC 4.2.2.2) 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-α-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.[1]

This enzyme catalyzes the chemical reaction

Eliminative cleavage of (1→4)-α-D-galacturonan to give oligosaccharides with 4-deoxy-α-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,.[2][3] 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.[4] 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.[5] 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);[6] Cry j I, a major allergenic glycoprotein of Cryptomeria japonica (Japanese cedar)—the most common pollen allergen in Japan;[7] and P56 and P59, which share sequence similarity with pectate lyases of plant pathogenic bacteria.[1]

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.

References

  1. ^ a b 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): 17–28. doi:10.1007/BF00015651. PMID 1983191.
  2. ^ Kamen DE, Woody RW (2002). "Folding kinetics of the protein pectate lyase C reveal fast-forming intermediates and slow proline isomerization". Biochemistry. 41 (14): 4713–4723. doi:10.1021/bi0115129. PMID 11926834.
  3. ^ Yoder MD, Keen NT, Jurnak F (1993). "New domain motif: the structure of pectate lyase C, a secreted plant virulence factor". Science. 260 (5113): 1503–1507. doi:10.1126/science.8502994. PMID 8502994.
  4. ^ WHO/IUIS Allergen Nomenclature Subcommittee (King TP, Hoffmann D, Loewenstein H, Marsh DG, Platts-Mills TAE, Bull TW). World Health Organ. 72:797–806 (1994).
  5. ^ 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 α II. Recombinant expression and reactivity with T cells from ragweed allergic patients". J. Immunol. 147 (8): 2547–2552. PMID 1717566.
  6. ^ 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): 493–502. doi:10.1007/BF00040608. PMID 1421152.
  7. ^ 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): 198–202. doi:10.1159/000236826. PMID 7920021.
This article incorporates text from the public domain Pfam and InterPro: IPR002022

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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.

Literature references

  1. Yoder MD, Keen NT, Jurnak F; , Science 1993;260:1503-1507.: New domain motif: the structure of pectate lyase C, a secreted plant virulence factor. PUBMED:8502994 EPMC:8502994


Internal database links

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 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(5)
Full
(7667)
Representative proteomes UniProt
(16276)
RP15
(687)
RP35
(3283)
RP55
(6156)
RP75
(9995)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(5)
Full
(7667)
Representative proteomes UniProt
(16276)
RP15
(687)
RP35
(3283)
RP55
(6156)
RP75
(9995)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(5)
Full
(7667)
Representative proteomes UniProt
(16276)
RP15
(687)
RP35
(3283)
RP55
(6156)
RP75
(9995)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

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.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: SCOP
Previous IDs: pec_lyase; Pec_lyase_C;
Type: Repeat
Sequence Ontology: SO:0001068
Author: Bateman A
Number in seed: 5
Number in full: 7667
Average length of the domain: 187.60 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 43.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 211
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Structures

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.

Loading structure mapping...

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.

Protein Predicted structure External Information
A0A0P0VA72 View 3D Structure Click here
A0A0P0WS98 View 3D Structure Click here
A0A0P0XED9 View 3D Structure Click here
A0A0P0XVJ6 View 3D Structure Click here
A0A0R0E8X8 View 3D Structure Click here
A0A0R0ERP7 View 3D Structure Click here
A0A0R0EU75 View 3D Structure Click here
A0A0R0FYJ4 View 3D Structure Click here
A0A0R0GR01 View 3D Structure Click here
A0A0R0GUZ0 View 3D Structure Click here
A0A0R0HPC7 View 3D Structure Click here
A0A0R0HUQ2 View 3D Structure Click here
A0A0R0I1P6 View 3D Structure Click here
A0A0R0I7K3 View 3D Structure Click here
A0A0R0K9E7 View 3D Structure Click here
A0A0R0LCI5 View 3D Structure Click here
A0A1D6EFG0 View 3D Structure Click here
A0A1D6G9Y5 View 3D Structure Click here
A0A1D6HEQ2 View 3D Structure Click here
A0A1D6HEQ3 View 3D Structure Click here
A0A1D6J4K9 View 3D Structure Click here
A0A1D6KU41 View 3D Structure Click here
A0A1D6LSL8 View 3D Structure Click here
A0A1D6N7M8 View 3D Structure Click here
A0A1D6N9K4 View 3D Structure Click here
A0A1D6P2H6 View 3D Structure Click here
B3LF89 View 3D Structure Click here
B6TPL1 View 3D Structure Click here
C0HEW0 View 3D Structure Click here
F4JW80 View 3D Structure Click here
I1J5K9 View 3D Structure Click here
I1JBP5 View 3D Structure Click here
I1JPR5 View 3D Structure Click here
I1JXE5 View 3D Structure Click here
I1K070 View 3D Structure Click here
I1K2L2 View 3D Structure Click here
I1KC87 View 3D Structure Click here
I1KZU9 View 3D Structure Click here
I1LAJ4 View 3D Structure Click here
I1LEZ6 View 3D Structure Click here
I1LNE4 View 3D Structure Click here
I1LNE5 View 3D Structure Click here
I1MFJ5 View 3D Structure Click here
I1MUL0 View 3D Structure Click here
I1MYL5 View 3D Structure Click here
I1N2D3 View 3D Structure Click here
I1N4A9 View 3D Structure Click here
I1N629 View 3D Structure Click here
I1NFF3 View 3D Structure Click here
K7KP94 View 3D Structure Click here
K7L9R5 View 3D Structure Click here
K7LAU1 View 3D Structure Click here
K7LNC8 View 3D Structure Click here
K7LZJ1 View 3D Structure Click here
K7MJD5 View 3D Structure Click here
K7MPC4 View 3D Structure Click here
O64510 View 3D Structure Click here
O65388 View 3D Structure Click here
O65456 View 3D Structure Click here
O65457 View 3D Structure Click here
Q0DEM8 View 3D Structure Click here
Q0DJF3 View 3D Structure Click here
Q43862 View 3D Structure Click here
Q5VP91 View 3D Structure Click here
Q6H8B0 View 3D Structure Click here
Q8RYR4 View 3D Structure Click here
Q93WF1 View 3D Structure Click here
Q93Z04 View 3D Structure Click here
Q93Z25 View 3D Structure Click here
Q940Q1 View 3D Structure Click here
Q944R1 View 3D Structure Click here
Q9C5M8 View 3D Structure Click here
Q9C8G4 View 3D Structure Click here
Q9FM66 View 3D Structure Click here
Q9FXD8 View 3D Structure Click here
Q9FY87 View 3D Structure Click here
Q9LFP5 View 3D Structure Click here
Q9LJ42 View 3D Structure Click here
Q9LRM5 View 3D Structure Click here
Q9LTZ0 View 3D Structure Click here
Q9M8Z8 View 3D Structure Click here
Q9M9S2 View 3D Structure Click here
Q9SCP2 View 3D Structure Click here
Q9SF49 View 3D Structure Click here
Q9SRH4 View 3D Structure Click here
Q9SVQ6 View 3D Structure Click here