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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 2018_03 genome PDB chains (SCOP 1.75)
Domains 8,641 68,017 7
Proteins 7,680 59,201 7


Functional annotation
General category Processes_EC
Detailed category Cell adhesion

Document:
Function annotation of SCOP domain superfamilies

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

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.007945Least InformativeInherited
Disease Ontology (DO)nervous system disease0.1216Least InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.000006861Moderately InformativeDirect
Disease Ontology (DO)lower respiratory tract disease0.00001319Moderately InformativeDirect
Disease Ontology (DO)cell type cancer0.0004998Moderately InformativeDirect
Disease Ontology (DO)artery disease0.00116Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.002648Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.006864Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.007823Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.02919Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.03152Moderately InformativeInherited
Disease Ontology (DO)disease of metabolism0.07032Moderately InformativeInherited
Disease Ontology (DO)connective tissue disease0.454Moderately InformativeInherited
Disease Ontology (DO)female reproductive system disease0.00000004379InformativeDirect
Disease Ontology (DO)prostate cancer0.0000001571InformativeDirect
Disease Ontology (DO)myopia0.0000008179InformativeDirect
Disease Ontology (DO)carcinoma0.000001601InformativeDirect
Disease Ontology (DO)atherosclerosis0.00001303InformativeDirect
Disease Ontology (DO)intrinsic cardiomyopathy0.00001618InformativeDirect
Disease Ontology (DO)primary bacterial infectious disease0.0001872InformativeDirect
Disease Ontology (DO)myeloid neoplasm0.0002053InformativeDirect
Disease Ontology (DO)breast cancer0.0003569InformativeDirect
Disease Ontology (DO)liver carcinoma0.0007472InformativeDirect
Disease Ontology (DO)arthritis0.0007854InformativeDirect
Disease Ontology (DO)cell type benign neoplasm0.0009003InformativeDirect
Disease Ontology (DO)connective tissue cancer0.001479InformativeInherited
Disease Ontology (DO)rheumatic disease0.001747InformativeInherited
Disease Ontology (DO)head and neck carcinoma0.001907InformativeInherited
Disease Ontology (DO)collagen disease0.004213InformativeInherited
Disease Ontology (DO)malignant glioma0.01037InformativeInherited
Disease Ontology (DO)urinary system cancer0.01381InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.09784InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.9429InformativeInherited
Disease Ontology (DO)muscle tissue disease0.9526InformativeInherited
Disease Ontology (DO)adult astrocytic tumour0.0000001461Highly InformativeDirect
Disease Ontology (DO)chondrosarcoma0.0000002182Highly InformativeDirect
Disease Ontology (DO)salivary gland adenoid cystic carcinoma0.000001564Highly InformativeDirect
Disease Ontology (DO)abdominal aortic aneurysm0.000002459Highly InformativeDirect
Disease Ontology (DO)ovary epithelial cancer0.000002791Highly InformativeDirect
Disease Ontology (DO)Kawasaki disease0.000005459Highly InformativeDirect
Disease Ontology (DO)Barrett's esophagus0.0000354Highly InformativeDirect
Disease Ontology (DO)dermatomyositis0.0000431Highly InformativeDirect
Disease Ontology (DO)renal cell carcinoma0.00007482Highly InformativeDirect
Disease Ontology (DO)bile duct adenocarcinoma0.0001513Highly InformativeDirect
Disease Ontology (DO)integumentary system cancer0.0002444Highly InformativeDirect
Disease Ontology (DO)bronchiectasis0.0003833Highly InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0005062Highly InformativeDirect
Disease Ontology (DO)head and neck squamous cell carcinoma0.0005728Highly InformativeDirect
Disease Ontology (DO)pancreatic ductal adenocarcinoma0.0009401Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of limbs0.1587Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.8835Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.1516Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of long bone morphology0.09341InformativeInherited
Phenotypic Abnormality (PA)Metaphyseal widening0.0001275Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0.005309Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.05808Least InformativeInherited
Mammalian Phenotype (MP)neoplasm0.01398Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.02472Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.04699Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.06595Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.06826Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.08562Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7618Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.9022Moderately InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to bacterial infection0.0000006695InformativeDirect
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.0003119InformativeDirect
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.004032InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.004585InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.009207InformativeInherited
Mammalian Phenotype (MP)joint inflammation0.01225InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.01295InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.01666InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.04943InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.05273InformativeInherited
Mammalian Phenotype (MP)altered tumor pathology0.06825InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.06933InformativeInherited
Mammalian Phenotype (MP)abnormal lung morphology0.2205InformativeInherited
Mammalian Phenotype (MP)decreased angiogenesis0.00007119Highly InformativeDirect
Mammalian Phenotype (MP)decreased tumor growth/size0.0001307Highly InformativeDirect
Mammalian Phenotype (MP)abnormal long bone hypertrophic chondrocyte zone0.000181Highly InformativeDirect
Mammalian Phenotype (MP)arthritis0.000269Highly InformativeDirect
Mammalian Phenotype (MP)decreased length of long bones0.0005147Highly InformativeDirect
Mammalian Phenotype (MP)aneurysm0.001179Highly InformativeInherited
Mammalian Phenotype (MP)abnormal pulmonary alveolus morphology0.00879Highly InformativeInherited
Mammalian Phenotype (MP)abnormal hindlimb morphology0.008833Highly InformativeInherited
Mammalian Phenotype (MP)abnormal retinal vasculature morphology0.02128Highly InformativeInherited
Mammalian Phenotype (MP)abnormal maxilla morphology0.1865Highly InformativeInherited
Mammalian Phenotype (MP)abnormal limb long bone morphology0.4107Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)pericellular component development variant0Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant0InformativeDirect

Document: WP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)anatomical cluster0Moderately InformativeDirect
Zebrafish Anatomy (ZA)skeletal system0.0003446InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds1Moderately InformativeInherited
Enzyme Commission (EC)Metalloendopeptidases0InformativeDirect
Enzyme Commission (EC)In linear amides0.000001089InformativeDirect
Enzyme Commission (EC)N-acetylmuramoyl-L-alanine amidase0Highly InformativeDirect

Document: EC 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 7 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 7 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]