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InterPro: IPR012334 Pectin lyase fold

Protein matches Help

UniProtKB

Matches:

5647 proteins

Overview:	sorted by AC,	sorted by name,	of known structure,	proteins with splice variants
Detailed:	sorted by AC,	sorted by name,	of known structure	proteins with splice variants
Table:	For all matching proteins,	of known structure
Architectures
Accession List
Matches in BioMart

Accession

IPR012334 Pectin_lyas_fold

Type

Domain

Signatures Help

Database	ID	Name	Proteins
Gene3D	G3DSA:2.160.20.10	Pectin_lyas_fold	5647
Signatures in BioMart

InterPro Relationships Help

Parent

IPR011050 Pectin lyase fold/virulence factor

Children

IPR000070 Pectinesterase, catalytic
IPR002022 Pectate lyase/Amb allergen
IPR004898 Pectate lyase, catalytic
IPR018082 AmbAllergen

Found in

IPR000743 Glycoside hydrolase, family 28
IPR005192 Glycoside hydrolase, family 49

Contains

IPR006626 Parallel beta-helix repeat
IPR018040 Pectinesterase, active site

InterPro annotation

Entry Details in BioMart

Abstract

This entry covers proteins that are closely related to the pectolytic enzyme, pectin lyase, which act as virulence factors. These proteins include pectate lyase, iota-carrageenase, and glycoside hydrolases from family 28 (such as galacturonases). Pectin lyases, pectate lyases and galacturonases all act on forms of pectin, one of the main components of the cell wall. When the backbone of pectin is methylated it is known as pectin, and can be cleaved by pectin lyase, a microbial virulence factor [1]. When the backbone of pectin is demethylated it is known as pectate, and can be cleaved by pectate lyase virulence factors, or hydrolysed by polygalacturonases [2, 3]. Iota-carrageenase is an enzyme that degrades carrageenan, a main component of the cell walls of various marine red algae. Unlike other carrageenase enzymes, iota-carrageenase belongs to the glycoside hydrolase structural family [4]. All these enzymes display a beta-helical structure.

Structural links Help

PDB - click here

SCOP: b.80.1.1 , b.80.1.10 , b.80.1.11 , b.80.1.2 , b.80.1.3 , b.80.1.4 , b.80.1.5 , b.80.1.8 , b.80.1.9

CATH: 2.160.20.10

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR012334

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

O04953 Putative pectinesterase 52

O97400 Polygalacturonase

P04960 Pectate lyase E

P20345 Pre-neck appendage protein

P47180 Polygalacturonase

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR012334	Pectin lyase fold
IPR018040	Pectinesterase, active site
IPR000070	Pectinesterase, catalytic
IPR000743	Glycoside hydrolase, family 28
IPR006626	Parallel beta-helix repeat
IPR011050	Pectin lyase fold/virulence factor
IPR002022	Pectate lyase/Amb allergen
	SWISS-MODEL
	PDB Chain
	ModBase
	SCOP Domain

Publications Open in usermanual
1.	Mayans O, Scott M, Connerton I, Gravesen T, Benen J, Visser J, Pickersgill R, Jenkins J. 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 1997 [PubMed: 9195887] http://dx.doi.org/10.1016/S0969-2126(97)00222-0
2.	Marin-Rodriguez MC, Orchard J, Seymour GB. Pectate lyases, cell wall degradation and fruit softening. J. Exp. Bot. 53 2115-9 2002 [PubMed: 12324535] http://dx.doi.org/10.1093/jxb/erf089
3.	Cho SW, Lee S, Shin W. The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex. J. Mol. Biol. 311 863-78 2001 [PubMed: 11518536] http://dx.doi.org/10.1006/jmbi.2001.4919
4.	Michel G, Chantalat L, Fanchon E, Henrissat B, Kloareg B, Dideberg O. The iota-carrageenase of Alteromonas fortis. A beta-helix fold-containing enzyme for the degradation of a highly polyanionic polysaccharide. J. Biol. Chem. 276 40202-9 2001 [PubMed: 11493601] http://intl.jbc.org/cgi/content/abstract/276/43/40202

Additional Reading Open in usermanual
	Xiao Z, Bergeron H, Grosse S, Beauchemin M, Garron ML, Shaya D, Sulea T, Cygler M, Lau PC. Improvement of the thermostability and activity of a pectate lyase by single amino acid substitutions, using a strategy based on melting-temperature-guided sequence alignment. Appl. Environ. Microbiol. 74 2008 1183-9 [PubMed: 18156340] http://dx.doi.org/10.1128/AEM.02220-07
	Di Matteo A, Giovane A, Raiola A, Camardella L, Bonivento D, De Lorenzo G, Cervone F, Bellincampi D, Tsernoglou D. Structural basis for the interaction between pectin methylesterase and a specific inhibitor protein. Plant Cell 17 2005 849-58 [PubMed: 15722470] http://dx.doi.org/10.1105/tpc.104.028886
	Mizuno M, Koide A, Yamamura A, Akeboshi H, Yoshida H, Kamitori S, Sakano Y, Nishikawa A, Tonozuka T. Crystal structure of Aspergillus niger isopullulanase, a member of glycoside hydrolase family 49. J. Mol. Biol. 376 2008 210-20 [PubMed: 18155243] http://dx.doi.org/10.1016/j.jmb.2007.11.098
	Fries M, Ihrig J, Brocklehurst K, Shevchik VE, Pickersgill RW. Molecular basis of the activity of the phytopathogen pectin methylesterase. EMBO J. 26 2007 3879-87 [PubMed: 17717531] http://dx.doi.org/10.1038/sj.emboj.7601816
	Bonivento D, Pontiggia D, Matteo AD, Fernandez-Recio J, Salvi G, Tsernoglou D, Cervone F, Lorenzo GD, Federici L. Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins. Proteins 70 2008 294-9 [PubMed: 17876815] http://dx.doi.org/10.1002/prot.21610

InterPro 23.1