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57  structures 1235  species 0  interactions 8032  sequences 229  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

In enzymology, a pectate lyase (EC 4.2.2.2) is an enzyme that catalyzes the chemical reaction

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.

Structural studies

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.

References

Template:Enzyme references

  • ALBERSHEIM P, KILLIAS U (1962). "Studies relating to the purification and properties of pectin transeliminase". Arch. Biochem. Biophys. 97: 107–15. PMID 13860094.
  • EDSTROM RD, PHAFF HJ (1964). "PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS". J. Biol. Chem. 239: 2403–8. PMID 14235514.
  • EDSTROM RD, PHAFF HJ (1964). "ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE". J. Biol. Chem. 239: 2409–15. PMID 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: 178–85. 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: 677–89. PMID 9195887.

External links

The CAS registry number for this enzyme class is Template:CAS registry.

Template:Enzyme links

Gene Ontology (GO) codes

Template:GO code links

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...

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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...

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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
(8032)
Representative proteomes UniProt
(17414)
RP15
(862)
RP35
(3445)
RP55
(6821)
RP75
(10848)
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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
(8032)
Representative proteomes UniProt
(17414)
RP15
(862)
RP35
(3445)
RP55
(6821)
RP75
(10848)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(8032)
Representative proteomes UniProt
(17414)
RP15
(862)
RP35
(3445)
RP55
(6821)
RP75
(10848)
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: 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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 211
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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.

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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.

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
A0A175VNJ3 View 3D Structure Click here
A0A175VP10 View 3D Structure Click here
A0A175W999 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
A1CFS2 View 3D Structure Click here
A1CYB8 View 3D Structure Click here
A1CYC2 View 3D Structure Click here
A1DEH0 View 3D Structure Click here
A2QFN7 View 3D Structure Click here
A2QV36 View 3D Structure Click here
A2QW65 View 3D Structure Click here
A2R3I1 View 3D Structure Click here
A2R6A1 View 3D Structure Click here
A2RBL2 View 3D Structure Click here
B3LF89 View 3D Structure Click here