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Pectin lyase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Single-stranded right-handed beta-helix [ 51125] (8)
Superfamily:   Pectin lyase-like [ 51126] (11)
Families:   Pectate lyase-like [ 51127] (2)
  Pectin lyase [ 51133]
  Galacturonase [ 51137] (2)
  Chondroitinase B [ 51144]
  iota-carrageenase [ 69333]
  Pectate transeliminase [ 101951]
  Dextranase, catalytic domain [ 101954]
  Pectin methylesterase [ 51147]
  P22 tailspike protein [ 51150]
  Virulence factor P.69 pertactin [ 51153]
  Filamentous hemagglutinin FhaB, secretion domain [ 101957]


Superfamily statistics
Genomes (2,373) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 31,250 146,726 36
Proteins 26,144 120,194 36


Functional annotation
General category Metabolism
Detailed category Polysaccharide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)primary metabolic process0.000000000052320.00001956Least InformativeDirect
Biological Process (BP)organic substance catabolic process00Moderately InformativeDirect
Biological Process (BP)carbohydrate metabolic process00Moderately InformativeDirect
Biological Process (BP)carbohydrate catabolic process00InformativeDirect
Biological Process (BP)polysaccharide metabolic process00InformativeDirect
Biological Process (BP)polysaccharide catabolic process00Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.000024750.0000000001481Least InformativeDirect
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds11Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on glycosyl bonds00InformativeDirect
Molecular Function (MF)carboxylic ester hydrolase activity0.00021080.00000000026InformativeDirect
Molecular Function (MF)hydrolase activity, hydrolyzing O-glycosyl compounds00Highly InformativeDirect
Cellular Component (CC)membrane11Least InformativeInherited
Cellular Component (CC)intrinsic component of membrane0.54220.9152Moderately InformativeInherited
Cellular Component (CC)external encapsulating structure0.011630.00000006873InformativeInherited
Cellular Component (CC)plant-type cell wall0.00011210.0001247Highly InformativeDirect
Cellular Component (CC)anchored component of membrane0.00022760.0001711Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00001956 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) organic substance catabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) response to biotic stimulus 0.161 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.06314 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) defense response 0.6473 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate catabolic process 0 Informative Direct
Biological Process (BP) polysaccharide metabolic process 0 Informative Direct
Biological Process (BP) defense response to other organism 0.09897 Informative Inherited
Biological Process (BP) response to bacterium 0.328 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.9506 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.04367 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.8304 Informative Inherited
Biological Process (BP) growth 0.4334 Informative Inherited
Biological Process (BP) behavior 0.6871 Informative Inherited
Biological Process (BP) system process 0.7615 Informative Inherited
Biological Process (BP) polysaccharide catabolic process 0 Highly Informative Direct
Biological Process (BP) glycosaminoglycan metabolic process 0.0001786 Highly Informative Direct
Biological Process (BP) cell growth 0.001218 Highly Informative Inherited
Biological Process (BP) developmental growth involved in morphogenesis 0.00944 Highly Informative Inherited
Biological Process (BP) nervous system process 0.1758 Highly Informative Inherited
Biological Process (BP) single-organism behavior 0.1934 Highly Informative Inherited
Biological Process (BP) cell-cell signaling 0.4904 Highly Informative Inherited
Biological Process (BP) aminoglycan catabolic process 0.5338 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0000000001481 Least Informative Direct
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 0 Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.00000000026 Informative Direct
Molecular Function (MF) hydrolase activity, hydrolyzing O-glycosyl compounds 0 Highly Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cell projection 0.7004 Moderately Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.9152 Moderately Informative Inherited
Cellular Component (CC) external encapsulating structure 0.00000006873 Informative Direct
Cellular Component (CC) plant-type cell wall 0.0001247 Highly Informative Direct
Cellular Component (CC) anchored component of membrane 0.0001711 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0.0003098Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1Least InformativeInherited
Enzyme Commission (EC)Carboxylic ester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Glycosidases, i.e. enzymes hydrolyzing O- and S-gl0Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0.2093Moderately InformativeInherited
Enzyme Commission (EC)Acting on polysaccharides0InformativeDirect
Enzyme Commission (EC)Alpha-galactosidase0.0001044Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processVirulence0Moderately InformativeDirect
Biological processHost-virus interaction0.00000002985Moderately InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processPolysaccharide degradation0InformativeDirect
Biological processVirus entry into host cell0.02786InformativeInherited
Biological processViral immunoevasion0.5655InformativeInherited
Biological processModulation of host cell apoptosis by virus0.0000000003685Highly InformativeDirect
Biological processInhibition of host IRF3 by virus0.00000000276Highly InformativeDirect
Biological processModulation of host ubiquitin pathway by viral deubiquitinase0.000000008206Highly InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentVirion0.2264Moderately InformativeInherited
Cellular componentCell outer membrane0InformativeDirect
Cellular componentPeriplasm0InformativeDirect
Cellular componentHost cytoplasm0.00000001743InformativeDirect
Cellular componentCell wall0Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0.0005337Moderately InformativeDirect
DiseaseAllergen0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainRepeat0.0001665Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainTransmembrane beta strand0InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationProtease1Moderately InformativeInherited
Post-translational modificationGlycosidase0InformativeDirect
Post-translational modificationSerine protease0.000000004902InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationZymogen0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011050 SSF51126 Protein matches
Abstract

Microbial pectin and pectate lyases are virulence factors that degrade the pectic components of the plant cell wall [PubMed9195887]. When the backbone of pectin is methylated it is known as pectin and is cleaved by pectin lyase, and when it is demethylated it is known as pectate and is cleaved by pectate lyase. Pectin lyase from Aspergillus niger displays a single-stranded, right-handed parallel beta-helix topology , where each coil contains three beta-strands and three turn regions. Several other virulence factors share this beta-helix topology, although they vary in the number of coils, including bacterial pectate lyases, fungal and bacterial galacturonases (such as rhamnogalacturonase and polygalacturonase), chrondroitinase B from Flavobacterium sp., iota-carrageenase from Alteromonas sp., pectin methylesterase (PemA), P22 tailspike protein from Salmonella phage P22, and the virulence factor P.69 pertactin from Bordetella pertussis that mediates adhesion to target mammalian cells [PubMed9724625].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 24 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Pectin lyase-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 24 hidden Markov models representing the Pectin lyase-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]