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PGBD-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   PGBD-like [ 47089]
Superfamily:   PGBD-like [ 47090] (2)
Families:   Peptidoglycan binding domain, PGBD [ 47091] (2)
  MMP N-terminal domain [ 63427] (4)


Superfamily statistics
Genomes (1,873) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 8,641 51,118 7
Proteins 7,680 44,609 7


Functional annotation
General category Processes_EC
Detailed category Cell adhesion

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) multicellular organismal process 0.000000000115 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000005908 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000002796 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00006745 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0002079 Least Informative Direct
Biological Process (BP) primary metabolic process 0.5466 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.4493 Least Informative Inherited
Biological Process (BP) response to stimulus 0.002861 Least Informative Inherited
Biological Process (BP) biological regulation 0.5362 Least Informative Inherited
Biological Process (BP) single-organism catabolic process 0.00000000000006022 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.0001644 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0002063 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0002147 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.0003803 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.0005483 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.03406 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.1317 Moderately Informative Inherited
Biological Process (BP) immune system process 0.01626 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.05123 Moderately Informative Inherited
Biological Process (BP) reproduction 0.1004 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.06257 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.0223 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.9734 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.06937 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.0354 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.07095 Moderately Informative Inherited
Biological Process (BP) tissue development 0.003934 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.002376 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.01598 Moderately Informative Inherited
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) localization of cell 0.000000000001324 Informative Direct
Biological Process (BP) locomotion 0.00000000001148 Informative Direct
Biological Process (BP) regulation of locomotion 0.00000001648 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.00000003157 Informative Direct
Biological Process (BP) movement of cell or subcellular component 0.0000000521 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.0000004047 Informative Direct
Biological Process (BP) response to wounding 0.000003732 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.000005989 Informative Direct
Biological Process (BP) regulation of anatomical structure size 0.00008825 Informative Direct
Biological Process (BP) growth 0.00009623 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0001796 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.0001806 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.04349 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) cell development 1 Informative Inherited
Biological Process (BP) epithelium development 0.09033 Informative Inherited
Biological Process (BP) embryo development 0.4121 Informative Inherited
Biological Process (BP) post-embryonic development 0.3258 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.001933 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.2175 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.1625 Informative Inherited
Biological Process (BP) cell death 0.04407 Informative Inherited
Biological Process (BP) regulation of defense response 0.04923 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.9244 Informative Inherited
Biological Process (BP) single organism reproductive process 0.4992 Informative Inherited
Biological Process (BP) reproductive system development 0.6729 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.06114 Informative Inherited
Biological Process (BP) central nervous system development 0.6291 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.1425 Informative Inherited
Biological Process (BP) multicellular organism metabolic process 0 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0 Highly Informative Direct
Biological Process (BP) programmed cell death involved in cell development 0.00000003118 Highly Informative Direct
Biological Process (BP) regeneration 0.0000004478 Highly Informative Direct
Biological Process (BP) ovulation cycle process 0.0000005778 Highly Informative Direct
Biological Process (BP) positive regulation of lymphocyte activation 0.00000177 Highly Informative Direct
Biological Process (BP) protein maturation 0.0000118 Highly Informative Direct
Biological Process (BP) response to hypoxia 0.00004014 Highly Informative Direct
Biological Process (BP) biological adhesion 0.00004244 Highly Informative Direct
Biological Process (BP) cell chemotaxis 0.00007532 Highly Informative Direct
Biological Process (BP) multi-multicellular organism process 0.00008236 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0.000101 Highly Informative Direct
Biological Process (BP) neuron development 0.0002636 Highly Informative Direct
Biological Process (BP) morphogenesis of an epithelium 0.0004058 Highly Informative Direct
Biological Process (BP) leukocyte migration 0.0004772 Highly Informative Direct
Biological Process (BP) regulation of leukocyte migration 0.007469 Highly Informative Inherited
Biological Process (BP) regulation of hemopoiesis 0.002191 Highly Informative Inherited
Biological Process (BP) sex differentiation 0.001026 Highly Informative Inherited
Biological Process (BP) wound healing 0.01072 Highly Informative Inherited
Biological Process (BP) developmental growth involved in morphogenesis 0.03925 Highly Informative Inherited
Biological Process (BP) establishment or maintenance of cell polarity 0.01301 Highly Informative Inherited
Biological Process (BP) post-embryonic animal morphogenesis 0.01153 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.002416 Highly Informative Inherited
Biological Process (BP) gastrulation 0.004178 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) metal ion binding 0.000000001287 Moderately Informative Direct
Molecular Function (MF) zinc ion binding 0 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.0000004218 Informative Direct
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.07473 Informative Inherited
Molecular Function (MF) metallopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) serine hydrolase activity 0.0000000000009673 Highly Informative Direct
Molecular Function (MF) peptidoglycan muralytic activity 0.0000000003799 Highly Informative Direct
Cellular Component (CC) membrane 0.909 Least Informative Inherited
Cellular Component (CC) extracellular region part 0.00000000000000156 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.001931 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.05746 Moderately Informative Inherited
Cellular Component (CC) neuron projection 0.00229 Informative Inherited
Cellular Component (CC) dendrite 0.000001935 Highly Informative Direct
Cellular Component (CC) anchored component of membrane 0.0001442 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)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)In linear amides0.0000006703Moderately InformativeDirect
Enzyme Commission (EC)Metalloendopeptidases0InformativeDirect
Enzyme Commission (EC)N-acetylmuramoyl-L-alanine amidase0Highly InformativeDirect
Enzyme Commission (EC)Gelatinase B0.00001086Highly InformativeDirect
Enzyme Commission (EC)Gelatinase A0.00001086Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processSporulation0.00000000000002778InformativeDirect
Biological processAngiogenesis0.000000000009955InformativeDirect
Biological processCell wall biogenesis/degradation0.0000000004183InformativeDirect
Cellular componentMembrane0.00009372Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix0InformativeDirect
Cellular componentGPI-anchor0.0000000008529InformativeDirect
DomainSignal0Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationZymogen0InformativeDirect
Post-translational modificationAutocatalytic cleavage0.0000000004823InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR002477 SSF47090 Protein matches
Abstract

This entry represents peptidoglycan binding domain (PGBD), as well as related domains that share the same structure. PGBD may have a general peptidoglycan binding function, has a core structure consisting of a closed, three-helical bundle with a left-handed twist. It is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [PubMed9555893, PubMed7121588, PubMed1683402]. Examples are:

  • Muramoyl-pentapeptide carboxypeptidase
  • N-acetylmuramoyl-L-alanine amidase cwlA precursor (cell wall hydrolase, autolysin, )
  • Autolytic lysozyme (1,4-beta-N-acetylmuramidase, autolysin, )
  • Membrane-bound lytic murein transglycosylase B
  • Zinc-containing D-alanyl-D-alanine-cleaving carboxypeptidase, VanX [PubMed6743245].

Many of the proteins having this domain are as yet uncharacterised. However, some are known to belong to MEROPS peptidase family M15 (clan MD), subfamily M15A metallopeptidases. A number of the proteins belonging to subfamily M15A are non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.

Eukaryotic enzymes can contain structurally similar PGBD-like domains. Matrix metalloproteinases (MMP), which catalyse extracellular matrix degradation, have N-terminal domains that resemble PGBD. Examples are gelatinase A (MMP-2), which degrades type IV collagen [PubMed10190290], stromelysin-1 (MMP-3), which plays a role in arthritis and tumour invasion [PubMed12810425, PubMed12888258], and gelatinase B (MMP-9) secreted by neutrophils as part of the innate immune defence mechanism [PubMed12950257]. Several MMPs are implicated in cancer progression, since degradation of the extracellular matrix is an essential step in the cascade of metastasis [PubMed11956636].


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-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 6 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 PGBD-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 6 hidden Markov models representing the PGBD-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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]