SUPERFAMILY 1.75 HMM library and genome assignments server

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 (1,867) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,617 34,237 7
Proteins 7,659 31,268 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) protein metabolic process 0.00000007473 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.000000000001121 Least Informative Direct
Biological Process (BP) developmental process 0.0000000001754 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0009802 Least Informative Direct
Biological Process (BP) localization 0.2076 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.06101 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.1753 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.01454 Least Informative Inherited
Biological Process (BP) response to stimulus 0.2654 Least Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.00001153 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.0007104 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0007657 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.9119 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.2201 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.02875 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.05257 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.003862 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.02622 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.181 Moderately Informative Inherited
Biological Process (BP) organ development 0.02094 Moderately Informative Inherited
Biological Process (BP) tissue development 0.04397 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.03389 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.00000000000606 Informative Direct
Biological Process (BP) cellular component movement 0.00000584 Informative Direct
Biological Process (BP) cell proliferation 0.0002605 Informative Direct
Biological Process (BP) organ morphogenesis 0.0000005821 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.0004925 Informative Direct
Biological Process (BP) locomotion 0.00000169 Informative Direct
Biological Process (BP) regulation of locomotion 0.000000002559 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.00008785 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.0000000003009 Informative Direct
Biological Process (BP) protein maturation 0.00006702 Informative Direct
Biological Process (BP) localization of cell 0.000000001533 Informative Direct
Biological Process (BP) tube development 0.04201 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.007955 Informative Inherited
Biological Process (BP) epithelium development 0.9813 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.4766 Informative Inherited
Biological Process (BP) embryonic organ development 0.006892 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.003958 Informative Inherited
Biological Process (BP) response to lipid 0.02672 Informative Inherited
Biological Process (BP) response to acid chemical 0.006312 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.6438 Informative Inherited
Biological Process (BP) single organism reproductive process 0.1583 Informative Inherited
Biological Process (BP) reproductive structure development 0.9042 Informative Inherited
Biological Process (BP) multi-multicellular organism process 0.001683 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.1959 Informative Inherited
Biological Process (BP) skeletal system development 0.00000000000001246 Highly Informative Direct
Biological Process (BP) ossification 0.0000000000002848 Highly Informative Direct
Biological Process (BP) response to hypoxia 0.00003282 Highly Informative Direct
Biological Process (BP) female pregnancy 0.000002443 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0 Highly Informative Direct
Biological Process (BP) ovulation cycle process 0.000002736 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) respiratory tube development 0.00001916 Highly Informative Direct
Biological Process (BP) zymogen activation 0.00000000003305 Highly Informative Direct
Biological Process (BP) collagen metabolic process 0 Highly Informative Direct
Biological Process (BP) response to amino acid 0.000039 Highly Informative Direct
Biological Process (BP) multicellular organismal catabolic process 0 Highly Informative Direct
Biological Process (BP) development of primary female sexual characteristics 0.000001398 Highly Informative Direct
Biological Process (BP) branching morphogenesis of an epithelial tube 0.0000000444 Highly Informative Direct
Biological Process (BP) respiratory system development 0.0000006465 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 0.08903 Highly Informative Inherited
Biological Process (BP) gonad development 0.01059 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.9416 Highly Informative Inherited
Biological Process (BP) post-embryonic organ development 0.1996 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) cation binding 0.00000000005666 Moderately Informative Direct
Molecular Function (MF) enzyme regulator activity 0.01452 Moderately Informative Inherited
Molecular Function (MF) enzyme activator activity 0.0004263 Informative Direct
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) zinc ion binding 0 Informative Direct
Molecular Function (MF) protein complex binding 0.00000434 Informative Direct
Molecular Function (MF) endopeptidase activity 0.0000004376 Highly Informative Direct
Molecular Function (MF) metallopeptidase activity 0 Highly Informative Direct
Cellular Component (CC) membrane 0.5604 Least Informative Inherited
Cellular Component (CC) extracellular region part 0.00000000003339 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.002448 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.2269 Moderately Informative Inherited
Cellular Component (CC) extracellular space 0.00007064 Informative Direct
Cellular Component (CC) neuron projection 0.0166 Informative Inherited
Cellular Component (CC) dendrite 0.0001215 Highly Informative Direct
Cellular Component (CC) anchored component of membrane 0.000002901 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

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.0126Least InformativeInherited
Disease Ontology (DO)immune system disease0.02414Least InformativeInherited
Disease Ontology (DO)nervous system disease0.129Least InformativeInherited
Disease Ontology (DO)obstructive lung disease0.0000001571Moderately InformativeDirect
Disease Ontology (DO)mouth disease0.0001339Moderately InformativeDirect
Disease Ontology (DO)artery disease0.0003726Moderately InformativeDirect
Disease Ontology (DO)skin disease0.000667Moderately InformativeDirect
Disease Ontology (DO)cell type cancer0.001419Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.003299Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.003568Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.01486Moderately InformativeInherited
Disease Ontology (DO)bacterial infectious disease0.0166Moderately InformativeInherited
Disease Ontology (DO)muscular disease0.0217Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.03643Moderately InformativeInherited
Disease Ontology (DO)disease of metabolism0.03899Moderately InformativeInherited
Disease Ontology (DO)connective tissue disease0.3015Moderately InformativeInherited
Disease Ontology (DO)female reproductive system disease0.000000008699InformativeDirect
Disease Ontology (DO)prostate cancer0.000001373InformativeDirect
Disease Ontology (DO)Kawasaki disease0.00000298InformativeDirect
Disease Ontology (DO)atherosclerosis0.000004InformativeDirect
Disease Ontology (DO)endometrial cancer0.000007299InformativeDirect
Disease Ontology (DO)primary bacterial infectious disease0.00008721InformativeDirect
Disease Ontology (DO)myeloma0.00009432InformativeDirect
Disease Ontology (DO)integumentary system cancer0.000126InformativeDirect
Disease Ontology (DO)arthritis0.0002975InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0003263InformativeDirect
Disease Ontology (DO)cell type benign neoplasm0.0004114InformativeDirect
Disease Ontology (DO)connective tissue cancer0.0007436InformativeDirect
Disease Ontology (DO)rheumatic disease0.001625InformativeInherited
Disease Ontology (DO)eye disease0.003613InformativeInherited
Disease Ontology (DO)collagen disease0.004166InformativeInherited
Disease Ontology (DO)urinary system cancer0.006977InformativeInherited
Disease Ontology (DO)heart disease0.01554InformativeInherited
Disease Ontology (DO)malignant glioma0.01653InformativeInherited
Disease Ontology (DO)esophageal disease0.02499InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.06295InformativeInherited
Disease Ontology (DO)myositis0.07602InformativeInherited
Disease Ontology (DO)gastrointestinal system cancer0.2223InformativeInherited
Disease Ontology (DO)adult astrocytic tumour0.00000006448Highly InformativeDirect
Disease Ontology (DO)ovary epithelial cancer0.0000007739Highly InformativeDirect
Disease Ontology (DO)abdominal aortic aneurysm0.000001258Highly InformativeDirect
Disease Ontology (DO)dermatomyositis0.00002487Highly InformativeDirect
Disease Ontology (DO)bronchiectasis0.0002804Highly InformativeDirect
Disease Ontology (DO)pancreatic ductal adenocarcinoma0.0006094Highly 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 skeletal morphology0.3107Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of long bone morphology0.006046InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the metaphyses0.0002176Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the epiphyses0.0008865Highly 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 phenotype0.01985Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.05747Least InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.01947Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.03587Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.1285Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1558Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.2665Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular development0.4449Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7529Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.9387Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.001794InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton physiology0.003684InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.013InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.01339InformativeInherited
Mammalian Phenotype (MP)abnormal bone structure0.01466InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.01772InformativeInherited
Mammalian Phenotype (MP)abnormal lung morphology0.04297InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.05079InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.05961InformativeInherited
Mammalian Phenotype (MP)abnormal cranium morphology0.1043InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to bacterial infection0.000004424Highly InformativeDirect
Mammalian Phenotype (MP)overexpanded pulmonary alveoli0.00006127Highly InformativeDirect
Mammalian Phenotype (MP)decreased angiogenesis0.0001061Highly InformativeDirect
Mammalian Phenotype (MP)decreased tumor growth/size0.0001779Highly InformativeDirect
Mammalian Phenotype (MP)arthritis0.0003943Highly InformativeDirect
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.0004512Highly InformativeDirect
Mammalian Phenotype (MP)aneurysm0.00159Highly InformativeInherited
Mammalian Phenotype (MP)abnormal maxilla morphology0.002827Highly InformativeInherited
Mammalian Phenotype (MP)abnormal hindlimb morphology0.005026Highly InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.005229Highly InformativeInherited
Mammalian Phenotype (MP)abnormal limb long bone morphology0.3252Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
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

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0.5626Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.805Least InformativeInherited
Xenopus ANatomical entity (XAN)surface structure0.1171Moderately InformativeInherited
Xenopus ANatomical entity (XAN)visual system0.9355Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.00003228Least InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage0.00005246Least InformativeDirect

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 (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.98Moderately InformativeInherited
Enzyme Commission (EC)Metalloendopeptidases0InformativeDirect
Enzyme Commission (EC)In linear amides0.0000008216InformativeDirect
Enzyme Commission (EC)N-acetylmuramoyl-L-alanine amidase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processSporulation0.000000000000004146InformativeDirect
Biological processAngiogenesis0.000000000003926InformativeDirect
Biological processCell wall biogenesis/degradation0.0000000009339InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein0.000000000001009Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues4.595e-16Moderately InformativeDirect
Post-translational modificationZymogen0InformativeDirect
Post-translational modificationAutocatalytic cleavage0.000000001089InformativeDirect

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