SUPERFAMILY 1.75 HMM library and genome assignments server


Penicillin-binding protein associated domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Penicillin-binding protein associated domain [ 69188]
Superfamily:   Penicillin-binding protein associated domain [ 69189] (2)
Families:   PBP5 C-terminal domain-like [ 69190] (2)
  Pencillin binding protein 4 (PbpD), C-terminal domain [ 110098]


Superfamily statistics
Genomes (1,418) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,247 20,836 4
Proteins 2,247 20,834 4


Functional annotation
General category Other
Detailed category Unknown function

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) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.003698 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.01163 Least Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0003607 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0004167 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.005107 Moderately Informative Inherited
Biological Process (BP) cell wall macromolecule metabolic process 0 Highly Informative Direct
Biological Process (BP) glycosaminoglycan metabolic process 0 Highly Informative Direct
Biological Process (BP) cellular component macromolecule biosynthetic process 0 Highly Informative Direct
Biological Process (BP) aminoglycan biosynthetic process 2.899e-11 Highly Informative Direct
Biological Process (BP) cell wall biogenesis 5.38e-07 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) exopeptidase activity 0 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)Serine-type carboxypeptidases0Highly InformativeDirect

Document: EC 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

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processCell shape0InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Cellular componentMembrane0.007525Least InformativeInherited
Cellular componentCell membrane1.194e-05Moderately InformativeDirect
Cellular componentCell inner membrane5.674e-08InformativeDirect
DomainSignal0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationCarboxypeptidase0Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cell wall metabolism0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)peptidoglycan biosynthesis0InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR015956 SSF69189 Protein matches
Abstract

This entry represents a structural motif found at the C-terminal of penicillin-binding proteins 4 (PBP4) and 5 (PBP5), as well as at the C-terminal of D-Ala-D-Ala carboxypeptidase A, a member of the MEROPS S11 peptidase family (PBP4 and PBP5 also belong to this peptidase family). These domains share a similar structure, consisting of a beta-sandwich of six strands in two sheets [PubMed14555648, PubMed15596446].

Penicillin-binding proteins are beta-lactam antibiotic-sensitive bacterial enzymes required for the growth and maintenance of the peptidoglycan layer of the bacterial cell wall that protects the cell from osmotic stress. PBP4 functions as a transpeptidase, acting co-operatively with PBP2 in staphylococcal cell wall biosynthesis and susceptibility to antimicrobial agents [PubMed16411754].


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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 3 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 Penicillin-binding protein associated domain 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 3 hidden Markov models representing the Penicillin-binding protein associated domain 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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]