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44  structures 449  species 0  interactions 1509  sequences 45  architectures

Family: Pec_lyase_C (PF00544)

Summary: Pectate lyase

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Pectate lyase Edit Wikipedia article

pectate lyase
Identifiers
EC number 4.2.2.2
CAS number 9015-75-2
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Pectate lyase/Amb allergen
Identifiers
Symbol Amb_allergen
Pfam PF00544
InterPro IPR002022
SMART SM00656

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-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.[1]

This enzyme 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

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 [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. 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 aI and Amb aII. The primary structure of Amb aII has been deduced and has been shown to share ~65% sequence identity with the Amb alpha I multigene family of allergens.[4] Members of the Amb aI/aII 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);[5] Cry jI, a major allergenic glycoprotein of Cryptomeria japonica (Japanese cedar) - the most common pollen allergen in Japan;[6] 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.

Structural studies[edit]

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[edit]

  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". 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. ^ 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 alpha II. Recombinant expression and reactivity with T cells from ragweed allergic patients". J. Immunol. 147 (8): 2547–2552. PMID 1717566. 
  5. ^ 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. 
  6. ^ Kojima K, Ogawa H, Hijikata A, Matsumoto I (1994). "Antigenicity of the oligosaccharide moiety of the Japanese cedar (Cryptomeria japonica) pollen allergen, Cry jI". Int. Arch. Allergy Immunol. 105 (2): 198–202. PMID 7920021. 
  • ALBERSHEIM P, KILLIAS U (1962). "Studies relating to the purification and properties of pectin transeliminase". Arch. Biochem. Biophys. 97 (1): 107–15. 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: 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 (2): 328. 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): 178–85. 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): 677–89. doi:10.1016/S0969-2126(97)00222-0. PMID 9195887. 

This article incorporates text from the public domain Pfam and InterPro IPR002022

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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.

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


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. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, 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 [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. 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 aI and Amb aII. The primary structure of Amb aII has been deduced and has been shown to share ~65% sequence identity with the Amb alpha I multigene family of allergens [PUBMED:1717566]. Members of the Amb aI/aII family include Nicotiana tabacum (Common tobacco) pectate lyase, which is similar to the deduced amino acid sequences of two pollen-specific pectate lyase genes identified in Solanum lycopersicum (Tomato) (Lycopersicon esculentum) [PUBMED:1421152]; Cry jI, a major allergenic glycoprotein of Cryptomeria japonica (Japanese cedar) - the most common pollen allergen in Japan [PUBMED:7920021]; and P56 and P59, which share sequence similarity with pectate lyases of plant pathogenic bacteria [PUBMED:1983191].

Domain organisation

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(10)
Full
(1509)
Representative proteomes NCBI
(1578)
Meta
(23)
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(220)
RP35
(471)
RP55
(647)
RP75
(752)
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  Seed
(10)
Full
(1509)
Representative proteomes NCBI
(1578)
Meta
(23)
RP15
(220)
RP35
(471)
RP55
(647)
RP75
(752)
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  Seed
(10)
Full
(1509)
Representative proteomes NCBI
(1578)
Meta
(23)
RP15
(220)
RP35
(471)
RP55
(647)
RP75
(752)
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Seed source: SCOP
Previous IDs: pec_lyase;
Type: Domain
Author: Bateman A
Number in seed: 10
Number in full: 1509
Average length of the domain: 190.70 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 45.93 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -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: 201
Family (HMM) version: 14
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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 Pec_lyase_C domain has been found. There are 44 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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